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The ocean sampling day consortium

  • Anna Kopf1, 2,
  • Mesude Bicak3,
  • Renzo Kottmann1,
  • Julia Schnetzer1, 2,
  • Ivaylo Kostadinov2,
  • Katja Lehmann4,
  • Antonio Fernandez-Guerra1, 3,
  • Christian Jeanthon5,
  • Eyal Rahav6,
  • Matthias Ullrich2,
  • Antje Wichels7,
  • Gunnar Gerdts7,
  • Paraskevi Polymenakou8,
  • Giorgos Kotoulas8,
  • Rania Siam9,
  • Rehab Z Abdallah9,
  • Eva C Sonnenschein10,
  • Thierry Cariou5,
  • Fergal O’Gara11, 12,
  • Stephen Jackson10,
  • Sandi Orlic14,
  • Michael Steinke15,
  • Julia Busch16,
  • Bernardo Duarte17,
  • Isabel Caçador17,
  • João Canning-Clode17, 18,
  • Oleksandra Bobrova19,
  • Viggo Marteinsson20,
  • Eyjolfur Reynisson20,
  • Clara Magalhães Loureiro21,
  • Gian Marco Luna22,
  • Grazia Marina Quero22,
  • Carolin R Löscher23,
  • Anke Kremp24,
  • Marie E DeLorenzo25,
  • Lise Øvreås26,
  • Jennifer Tolman27,
  • Julie LaRoche27,
  • Antonella Penna28,
  • Marc Frischer29,
  • Timothy Davis30,
  • Barker Katherine31,
  • Christopher P Meyer31,
  • Sandra Ramos32,
  • Catarina Magalhães32,
  • Florence Jude-Lemeilleur33,
  • Ma Leopoldina Aguirre-Macedo34,
  • Shiao Wang35,
  • Nicole Poulton36,
  • Scott Jones37,
  • Rachel Collin38,
  • Jed A Fuhrman39,
  • Pascal Conan40,
  • Cecilia Alonso41,
  • Noga Stambler42, 43,
  • Kelly Goodwin44,
  • Michael M Yakimov45,
  • Federico Baltar46,
  • Levente Bodrossy47,
  • Jodie Van De Kamp47,
  • Dion MF Frampton47,
  • Martin Ostrowski48,
  • Paul Van Ruth49,
  • Paul Malthouse49,
  • Simon Claus50,
  • Klaas Deneudt50,
  • Jonas Mortelmans50,
  • Sophie Pitois51,
  • David Wallom3,
  • Ian Salter40, 52,
  • Rodrigo Costa53,
  • Declan C Schroeder54,
  • Mahrous M Kandil55,
  • Valentina Amaral41,
  • Florencia Biancalana57,
  • Rafael Santana41,
  • Maria Luiza Pedrotti56,
  • Takashi Yoshida58,
  • Hiroyuki Ogata58,
  • Tim Ingleton60, 64,
  • Kate Munnik61,
  • Naiara Rodriguez-Ezpeleta62,
  • Veronique Berteaux-Lecellier63,
  • Patricia Wecker63,
  • Ibon Cancio65,
  • Daniel Vaulot5,
  • Christina Bienhold1, 52,
  • Hassan Ghazal67, 68,
  • Bouchra Chaouni68, 71,
  • Soumya Essayeh67,
  • Sara Ettamimi68, 70,
  • El Houcine Zaid71,
  • Noureddine Boukhatem68,
  • Abderrahim Bouali68,
  • Rajaa Chahboune67, 72,
  • Said Barrijal72,
  • Mohammed Timinouni74,
  • Fatima El Otmani75,
  • Mohamed Bennani74,
  • Marianna Mea2,
  • Nadezhda Todorova77,
  • Ventzislav Karamfilov77,
  • Petra ten Hoopen78,
  • Guy Cochrane78,
  • Stephane L’Haridon79,
  • Kemal Can Bizsel80,
  • Alessandro Vezzi81,
  • Federico M Lauro82,
  • Patrick Martin83,
  • Rachelle M Jensen84,
  • Jamie Hinks82,
  • Susan Gebbels85,
  • Riccardo Rosselli81,
  • Fabio De Pascale81,
  • Riccardo Schiavon81,
  • Antonina dos Santos59,
  • Emilie Villar13,
  • Stéphane Pesant87,
  • Bruno Cataletto88,
  • Francesca Malfatti88,
  • Ranjith Edirisinghe89,
  • Jorge A Herrera Silveira35,
  • Michele Barbier92,
  • Valentina Turk93,
  • Tinkara Tinta93,
  • Wayne J Fuller94,
  • Ilkay Salihoglu94,
  • Nedime Serakinci94,
  • Mahmut Cerkez Ergoren94,
  • Eileen Bresnan98,
  • Juan Iriberri65,
  • Paul Anders Fronth Nyhus100,
  • Edvardsen Bente101,
  • Hans Erik Karlsen102,
  • Peter N Golyshin103,
  • Josep M Gasol104,
  • Snejana Moncheva105,
  • Nina Dzhembekova105,
  • Zackary Johnson106,
  • Christopher David Sinigalliano44,
  • Maribeth Louise Gidley44, 107,
  • Adriana Zingone108,
  • Roberto Danovaro108, 109,
  • George Tsiamis110,
  • Melody S Clark111,
  • Ana Cristina Costa21,
  • Monia El Bour99,
  • Ana M Martins21, 95,
  • R Eric Collins96,
  • Anne-Lise Ducluzeau96,
  • Jonathan Martinez97,
  • Mark J Costello86,
  • Linda A Amaral-Zettler90, 91,
  • Jack A Gilbert69, 73, 76, 90,
  • Neil Davies2, 66,
  • Dawn Field2, 3 and
  • Frank Oliver Glöckner1, 2Email author
Contributed equally
GigaScience20154:27

https://doi.org/10.1186/s13742-015-0066-5

Received: 18 February 2015

Accepted: 6 May 2015

Published: 19 June 2015

Abstract

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Keywords

Ocean sampling day OSD Biodiversity Genomics Health Index Bacteria Microorganism Metagenomics Marine Micro B3 Standards

Background

Marine microbes inhabit all marine habitats, are the engines of the ocean’s major biogeochemical cycles, and form the basis of the marine food web [1]. Over the past decades scientists have aimed to understand marine microorganisms, but technical and computational limitations have restricted studies to a local scale. Fortunately, with technological advancements and decreasing sequencing costs, genomic studies have become feasible on a global scale. The first landmark marine metagenome studies were published by the J Craig Venter Institute, beginning with a pilot sampling project in the Sargasso Sea followed by the Global Ocean Sampling (GOS) expedition [2]. The Tara Ocean project expanded this further by integrating the marine genetic, morphological, and functional biodiversity in its environmental context at global ocean scale and at multiple depths [3]. The Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project now aims to investigate global marine microbial biodiversity and has pioneered the idea to do this on a single orchestrated Ocean Sampling Day (OSD).

Main text

Ocean Sampling Day

OSD is a simultaneous, collaborative, global mega-sequencing campaign to analyze marine microbial community composition and functional traits on a single day. On June 21st 2014 – the world’s first major OSD event – scientists around the world collected 155 16S/18S rRNA amplicon data sets, 150 metagenomes, and a rich set of environmental metadata. Standardized procedures, including a centralized hub for laboratory work and data processing via the Micro B3 Information System (Micro B3-IS), assured a high level of consistency and data interoperability [4]. Application of the Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards ensures sustainable data storage and retrieval in respective domain-specific data archives [4]. OSD generated the largest standardized data set on marine microbes taken on a single day, which we consider complementary to other large-scale sequencing projects.

The solstice was chosen to test the hypothesis that diversity negatively correlates with day-length [5]. Data analysis will target three main areas: biodiversity, gene functions, and ecological models. OSD sampling sites are typically located in coastal regions within exclusive economic zones (EEZ). Therefore, the OSD data set provides a unique opportunity to test anthropogenic influences on microbial population ecology. We will perform a multi-level assessment of the human impact on microbial mediated biogeochemical cycles. Questions we would like to answer are: (i) what are the important factors (physical-chemical and biological) in structuring biodiversity patterns and range margins, and (ii) are functions associated with heavy metals, antibiotics or fecal indicators correlated with OSD sites exposed to higher human impact? We are confident that the simultaneous collection of samples will result in the discovery of new ecological patterns providing key information towards understanding environmental vulnerability and resilience.

Open access strategy and sharing of data

All OSD data are archived and immediately made openly accessible without an embargo period, following the Fort Lauderdale rules for sharing data [6]. Sequence and contextual data are publicly available via the International Nucleotide Sequence Database Collaboration (INSDC) umbrella study PRJEB5129 and at PANGAEA. A model agreement and OSD Data Policy [4] was developed in compliance with the Convention on Biological Diversity and the Nagoya Protocol on Access and Benefit Sharing (ABS) for the utilization on genetic resources in a fair and equitable way. An ABS Helpdesk exists to support OSD participants’ legal questions. Furthermore, the Mediterranean Science Commission (CIESM) developed the CIESM Charter on ABS, which has been endorsed by 391 scientists from 49 countries (as of April 2015).

The OSD Consortium

At the 16th Genomics Standards Consortium (GSC) meeting in 2014, the OSD community agreed to form the OSD Consortium. Led by the five OSD Coordinators and comprising of up to 130 OSD Site Coordinators and their teams, the OSD Consortium installed the infrastructure and expertise allowing coordinated OSD events to take place. Furthermore, the OSD Consortium aims to foster collaborations and share expertise among and beyond the OSD network, and to connect scientists in a worldwide environmental movement.

Membership and governance

OSD membership is open to anyone and is earned by participation. Registered participants are provided with privileged access to the OSD network of sites, as well as training activities. OSD samples are prioritized for all types of data generation (as funds and resources allow). In return, participants agree to provide samples according to OSD’s standardized procedures and to work under the umbrella of the OSD Data Policy, which requires open sharing of data and to respect the national legal sampling framework.

The OSD network of sites

Participants from 191 sampling sites signed up for the main OSD event; these sites range from tropical waters to polar environments (Fig. 1). All major oceanic divisions (Pacific, Atlantic, Indian, Antarctic and Arctic Ocean) and continents are covered with 81 and 37 sites in Europe and North America, respectively. The majority of sites are located in the Northern Hemisphere (172), including 36 sites in the Mediterranean and three sites in the Black Sea.
Fig. 1

Map of registered sites for OSD 2014

OSD partnerships

Endorsement of the community and fruitful partnerships are essential. Supported by the Argonne National Laboratory, the generous cooperation with the Earth Microbiome Project (EMP) [7] enabled us to perform amplicon sequencing for OSD pilot events; these were conducted on each of the solstices in 2012 and 2013. In return, OSD data is EMP compliant and contributes towards construction of a global catalog of microbial diversity [7]. Cooperation with the LifeWatch project secured additional 18S rRNA gene sequencing, while Pacific Bioscience contributed sequencing of near-full-length 16S rRNA gene amplicons and metagenomes from selected OSD sampling sites. Moreover, the partnership with the Smithsonian Institute’s Global Genome Initiative for long-term bioarchiving of all OSD samples enables the community to re-analyze the samples in the future.

OSD beyond 2014

The OSD Consortium aims to expand in terms of sites and methods, as well as towards multicellular organisms. Future key tasks are to align closely with the Genomic Observatories (GOs) Network [8] towards biocoding the ocean, as well as to secure long-term resources and commitments to create an OSD time-series. The mid-term vision of the OSD Consortium is to generate microbial Essential Biodiversity Variables (EBV) data [9]. The envisioned regular OSD events would qualify for the candidate EBVs “Species populations” and “Community composition” to indicate, for example, vulnerability of ecosystems and climatic impacts on community composition. In the long term such indicators may be incorporated into the Ocean Health Index (OHI) [10], which currently excludes microorganisms from biodiversity assessment due to the lack of reliable data. OSD has the potential to close that gap and amend EBV and OHI by expanding oceanic monitoring towards microbes. This could lead to a global system of harmonized observations to inform scientists and policy-makers.

Conclusions

This commentary outlines the process for creating, managing and formalizing the OSD Consortium and describes its vision for a sustainable study of marine microbes. As we move forward, we will continue to explore and expand the scope of OSD beyond 2014. The idea of an OSD time-series is still in its early days but incorporating the OSD data set as EBVs and in the OHI is a strong source of motivation since this could pave the way to prioritize scientific research and raise public awareness for the unseen majority of the world’s oceans.

Notes

Abbreviations

ABS: 

Access and benefit sharing

CIESM: 

Mediterranean Science Commission (Commission Internationale pour l'Exploration Scientifique de la Méditerranée)

EBV: 

Essential biodiversity variables

EEZ: 

Exclusive economic zone

EMP: 

Earth microbiome project

GOs: 

Genomic observatories

GOS: 

Global ocean sampling expedition

Micro B3: 

Marine Microbial Biodiversity, Bioinformatics, Biotechnology

Micro B3-IS: 

Micro B3 information system

M2B3: 

Marine microbial biodiversity, bioinformatics and biotechnology data reporting and service standards

EBV: 

Essential biodiversity variables

OHI: 

Ocean health index

OSD: 

Ocean sampling day

rRNA: 

ribosomal RNA

Declarations

Acknowledgements

We wish to acknowledge our extensive range of Micro B3/OSD participants, partners, advisors and supporters who have made the OSD possible. The generosity and tremendous support from our partners and participants has not only enriched the data set but also allowed the OSD Consortium to save resources for future OSD activities. We would also like to thank Sandra Nowack, Hilke Döpke, Greta Reintjes, Timmy Schweer and the technicians of the Max Planck Institute for Marine Microbiology for their tremendous support with on-site logistics. This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589. This manuscript is NOAA-GLERL contribution number 1763.

Authors’ Affiliations

(1)
Max Planck Institute for Marine Microbiology
(2)
Jacobs University Bremen gGmbH
(3)
University of Oxford
(4)
Centre for Ecology & Hydrology, MacLean Building, Benson Lane
(5)
CNRS & Sorbonne Universités, UPMC Univ Paris 06
(6)
Israel Oceanographic and Limnological Research, National Institute of Oceanography
(7)
Alfred Wegener Institute, Biologische Anstalt Helgoland
(8)
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture
(9)
Biology Department and YJ-Science and Technology Research Center, American University in Cairo
(10)
Department of Systems Biology, Technical University of Denmark
(11)
National University of Ireland–University College Cork
(12)
Curtin University, Biomedical Sciences
(13)
Aix Marseille Université, CNRS, IGS UMR 7256
(14)
Ruđer Bošković Institute
(15)
School of Biological Sciences, University of Essex
(16)
Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg
(17)
Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon
(18)
Smithsonian Environmental Research Center
(19)
Department of Microbiology, Virology and Biotechnology, Odessa National II Mechnikov University
(20)
Matis Ltd
(21)
InBio/CIBIO, Departamento de Biologia da Universidade dos Açores
(22)
National Research Council, Institute of Marine Sciences (CNR-ISMAR)
(23)
Institute of Microbiology/ GEOMAR
(24)
Marine Research Centre, Finnish Environment Institute
(25)
NOAA/National Ocean Service/NCCOS/Center for Coastal Environmental Health & Biomolecular Research Charleston
(26)
Department of Biology, University of Bergen
(27)
LaRoche Research Group, Department of Biology, Dalhousie University
(28)
Department of Biomolecular Sciences, University of Urbino
(29)
University of Georgia’s Skidaway Institute of Oceanography
(30)
NOAA–Great Lakes Environmental Research Laboratory
(31)
National Museum of Natural History, Smithsonian Institution
(32)
CIIMAR, Interdisciplinary Center of Environmental and Marine Research, University of Porto
(33)
Station Marine d’Arcachon, CNRS & Univ Bordeaux
(34)
Centro de Investigación y de Estudios Avanzados (CINVESTAV), Unidad Mérida
(35)
Department of Biological Sciences, University of Southern Mississippi
(36)
Bigelow Laboratory for Ocean Sciences
(37)
Smithsonian Marine Station
(38)
Smithsonian Tropical Research Institute
(39)
Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California
(40)
Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique
(41)
Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República
(42)
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University
(43)
Interuniversity Institute for Marine Sciences in Eilat
(44)
NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division
(45)
Institute for Coastal Marine Environment, IAMC-CNR
(46)
Department of Marine Science, University of Otago
(47)
CSIRO Oceans and Atmosphere Flagship
(48)
Department of Chemistry and Biomolecular Science, Macquarie University
(49)
South Australian Research and Development Institute (SARDI) – Aquatic Sciences
(50)
Flanders Marine Institute, InnovOcean site
(51)
Centre for Environment, Fisheries and Aquaculture Science (CEFAS)
(52)
Alfred-Wegener-Institut-Helmholtz-Zentrum für Polar-und Meeresforschung
(53)
Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, Algarve University
(54)
Marine Biological Association of the UK
(55)
Soil and Water Science Department, Faculty of Agriculture, Alexandria University
(56)
Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7093, LOV, Observatoire océanologique, F-Villefranche-sur-Mer
(57)
Marine Biogeochemistry – Argentine Institute of Oceanography
(58)
Graduate School of Agriculture, Kyoto University
(59)
IPMA, Department of Sea and Marine Resources
(60)
Waters, Wetlands and Coasts, New South Wales Office of Environment and Heritage
(61)
Lwandle Technologies
(62)
Marine Research Division
(63)
CRIOBE, USR3278 CNRS-EPHE-UPVD
(64)
Antarctic and Southern Ocean Studies, University of Tasmania
(65)
University of the Basque Country
(66)
Gump South Pacific Research Station, University of California Berkeley
(67)
Polydisciplinary Faculty of Nador, University Mohammed Premier
(68)
Laboratory of Genetics and Biotechnology, University Mohammed Premier
(69)
College of Environmental and Resource Sciences, Zhejiang University
(70)
Polydisciplinary Faculty of Taza, University Sidi Mohammed Ben Abdallah
(71)
Faculty of Sciences of Rabat, University Mohammed Fifth Rabat
(72)
Faculté des Sciences et Techniques de Tanger, Université Abdelmalek Essaâdi
(73)
Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory
(74)
Pasteur Institute of Morocco
(75)
Microbiology, Health and Environment Team, Department of Biology, Faculty of Sciences, Chouaib Doukkali University
(76)
University of Chicago
(77)
Institute of Biodiversity and Ecosystem Research (IBER), Bulgarian Academy of Sciences
(78)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus
(79)
Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)
(80)
Dokuz Eylul University (DEU), Institute of Marine Sciences and Technology (IMST)
(81)
Department of Biology, University of Padova
(82)
Singapore Centre for Environmental Life Sciences Engineering
(83)
Earth Observatory of Singapore, Nanyang Technological University
(84)
Indigo V Expeditions, ONE°15 Marina
(85)
School of Marine Science and Technology, Newcastle University, Dove Marine Laboratory
(86)
Institute of Marine Science, University of Auckland
(87)
PANGAEA - Data Publisher for Earth & Environmental Science, MARUM Center for Marine Environmental Sciences, University Bremen
(88)
OGS, National Institute of Oceanography and Experimental Geophysics, Via Auguste Piccard
(89)
Department of Physical Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka
(90)
Marine Biological Laboratory
(91)
Department of Earth, Environmental, and Planetary Sciences, Brown University
(92)
Mediterranean Science Commission
(93)
Marine Biology Station, National Institute of Biology
(94)
Near East University
(95)
Department of Oceanography and Fisheries, University of the Azores
(96)
University of Alaska Fairbanks
(97)
University of Hawaii at Manoa, Kewalo Marine Laboratory
(98)
Phytoplankton Ecology, Marine Scotland Marine Laboratory
(99)
Institut National des Sciences et Technologies de la Mer (INSTM)
(100)
Kind of Blue Project ABS and Citizen Science
(101)
Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo
(102)
Drøbak Field Station, Marine Biology Research station
(103)
School of Biological Sciences, College of Natural Sciences, Bangor University
(104)
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC
(105)
Fridtjof Nansen Institute of Oceanology
(106)
Nicholas School of the Environment and Biology Department, Duke University
(107)
Cooperative Institute of Marine and Atmospheric Sciences, Rosenstiel School of Marine & Atmospheric Science, University of Miami
(108)
Stazione Zoologica Anton Dohrn
(109)
Department of Life and Environmental Sciences, Polytechnic University of Marche
(110)
Department of Environmental and Natural Resources Management, University of Patras
(111)
British Antarctic Survey, Natural Environment Research Council, High Cross

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Copyright

© Kopf et al. 2015

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.