Ocean Sampling Day | Assemble+

Ocean Sampling Day


The Ocean Sampling Day (OSD) is a simultaneous worldwide research campaign where marine biologists around the globe participate in sampling of the world’s oceans to produce contextual genomic data. OSD was launched by the MicroB3 project in the summer, on the solstice, 21 June 2014, with ASSEMBLE Plus taking on the OSD coordination in 2018. The OSD campaign is supported by the ASSEMBLE Plus coordinator, European Marine Biological Resource Centre and partner, the Hellenic Centre for Marine Research (HCMR) in Heraklion, Crete, who have coordinated OSD, received and processed all the samples as well as extracted and sequenced 16S and 18S rRNA. Shotgun metagenomics data have also been produced in GENOSCOPE, France.

Through Marine Biodiversity Observation Networks (MBONs) collecting cumulative samples, related in time, space and environmental parameters, researchers can gain invaluable insights into the marine environment, including insights into the changes in biodiversity as a result of climate change and the introduction of non-native species by shipping, etc. DNA analysis accomplished by using marker genes, allows us to identify all prokaryotic and eukaryotic microbial species in the water samples obtained, while analysis of metagenomic data allows us to assess the functional content and potential of bacterial communities. Among the many questions the data can answer, the basic ones include "what organisms are found where?" and "what functions can they fulfill, under the assessed environmental conditions?". All collections were carried out in a standardised way to allow comparability among samples and accurately track changes in the marine environment over time. The data collected is a reference data set for generations of experiments to follow in the coming decades. One particular project that has benefitted from OSD data is the European Marine Omics Biodiversity Observation Network (EMO BON), an EMBRC project aiming to enhance the European contribution to global genomic observation efforts.

An important effort was necessary to find the best ways to make the data open access and FAIR (Findable, Accessible, Interoperable and Reusable), this was achieved by collaboration between Flanders Marine Institute (VLIZ), the German Federation for Biological Data (GFBio) and HCMR. There is not a simple way to data FAIRification, as there is still room for improvement in the interoperability between databases hosting biodiversity and environmental data and databases hosting molecular data. OSD data FAIRification has inspired collaborative projects between the European infrastructures ASSEMBLE Plus coordinator European Marine Biological Resource Centre (EMBRC ERIC), ELIXIR Europe and LifeWatch ERIC within the context of the European Open Science Cloud (EOSC).

The cost of sequencing has been covered by EMBRC. The value of FAIR data will increase with time, as any new environmental dataset, can be compared to it, to add insights on marine biodiversity structure, function and dynamics. Also, as genomic data on single species will keep increasing and high quality genomic and biological annotation will be added, OSD data can be revisited and reanalysed delivering more knowledge, which may be still inaccessible under the actual state of things.

HCMR carries out some preliminary analysis on DNA metabarcoding of 16S rRNA data, to offer a small hint on the value of data. In parallel, the data are offered for exploration to the experts around the world. The OSD data can now be openly accessed in ASSEMBLE Plus partner, VLIZ’s Integrated Marine Information System (IMIS) and shortly in OBIS, GBIF and Pangea:

The data include enviromental measurements made during the sampling events at each sampling site and DNA sequences obtained from the collected water samples. The DNA data are published in the European Nucleotide Archive and their "accession numbers" are gathered together with the environmental measurements and sampling details on spreadsheets that can be found in the links given above. These  datasets and accompanying metadata are also available via the OSD GitHub Repository, which includes the different versions of the data including machine-interoperable versions suitable for developer access. These data are in compliance with H2020’s Open Research Data Pilot, following the FAIR (Findable, Interoperable, Accessible and Reusable) principles.

The OSD initiative in ASSEMBLE Plus was designed as a pilot study for a larger ‘omics-based observatory. EMBRC-ERIC, the Project Coordinator, is a research infrastructure dedicated to research and innovation from marine biological resources. To start producing regular biodiversity monitoring data, EMBRC is looking to invest in a more systematic manner in a sustainable ‘Omics Observatory and go beyond what has been initiated through ASSEMBLE Plus. In doing so, EMBRC is aiming to build a European observatory based on the OSD protocols, contributing to global efforts in genomics observation, and establishing interactions with other initiatives and communities, such as GSCGLOMICON and other research infrastructures (e.g. LifeWatch ERICe-LTERELIXIR). Continuing to work with the global OSD network, EMBRC wish to take steps for a more active communication and interaction with the partners, contributing to the improvement of OSD protocols, operation, and generation of Findable, Accessible, Interoperable, and Reproducible (FAIR) omics-based biodiversity data. This will also help to frame this broad initiative in a contributing manner towards the fulfillment of the UN 2030 Sustainable Development Goals

Looking deeper into the future

OSD will be strengthened thanks to the Horizon 2020-funded AtlantECO project that will support OSD 2022 and 2023, intensifying sampling in Southern Atlantic and including cruises for training the coastal labs on OSD protocols.

Those years we will try to have a denser coverage with stations along Atlantic coasts, and especially in Southern Atlantic to try and get an all-Atlantic view of coastal microbial diversity.

For the southern hemisphere, there is consensus within AtlantECO that the OSD should happen on 21st December on their side of the world so that we sample the summer solstice in both hemispheres.

Map of OSD participant sites since 2014

OSD 2021 Sampling Protocols and Metadata

We will follow the detailed Protocols A for prokaryotes and Protcols B for eukaryotes, as described in MicroB3 OSD Handbook v3.1 (April 2016). The protocols and log sheets for OSD2020 (as adapted from MicroB3 OSD Handbook v3.1) can be downloaded directly:

  • OSD 2021: Protocol A (.docx; .pdf)
  • OSD 2021: Protocol B  (.docx; .pdf)
  • OSD 2021: Log Sheets (.xlsx; .pdf)
Brief OSD2021 Pipeline
  1. Collect your samples following the OSD sampling protocol (using Sterivex filters for Prokaryotes or polycarbonate membrane filters for Eurkaryotes)
  2. Ship your filters to IMBBC-HCMR in Heraklion, Crete, in dry ice to the address provided in the 'Contact' section below.
  3. Provide us with relevant metadata. Please take notice of the mandatory metadata requirements for submission. Samples without metadata will not be processed, as they cannot be properly explored and compared to the rest of datasets.
  4. Please send your signed permits (see below) to the address below. Having these permits is a pre-requisit for the sampling and for transferring material! 
  5. In case you are experiencing serious problems with dry-ice shipment to Greece, please contact us at: osd-contact@embrc.eu
Legal Issues

All participants of Ocean Sampling Day 2021 (OSD2021) need to comply with Access and Benefit Sharing (ABS) requirements, as set out in the Convention on Biological Diversity (CBD) and the Nagoya Protocol (NP), and with the requirements laid out in the Material Transfer Agreement (MTA) and Data Policy documents, which cover the necessaries following the international law of the sea. Detailed instructions can be found in the OSD2021 Legal Permits Procedure. Please also refer to the detailed guide on the definitions of OSD metadata and instructions on how to complete the logsheets.

The following required documents to be filled in and signed by all participating teams, old and new:

The filled in and signed documents must be sent back to us:

  • electronically (print, sign, scan and send back as jpg or pdf) as soon as possible AND
  • as hard copies (shipped together with your samples to IMBBC-HCMR, see address above) by Friday 17th July 2021 

Remember that for each station sampled, a separate Data Policy Document should be signed and returned. 


For any questions, information, or assistance, contact the OSD-IMBBC team by sending an email to osd-contact@embrc.eu.

The IMBBC-HCMR persons of contact are: 

  • Melanthia (Melina) Stavroulaki Post-Doctoral Researcher at IMBBC (OSD Coordinator Contact)
  • Panagiotis Kasapidis Principal Researcher at IMBBC (OSD2020 Coordinator)
  • Georgios Kotoulas Research Director at IMBBC, JRA1 Coordinator

Postal Address: 

Dr Melanthia Stavroulaki
Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC)
Hellenic Centre for Marine Research (HCMR)
Gournes Pediados

71500, Heraklion
Greece (Hellas)

+30-2810-337801, +30-2810-337840
+30-2810-337719, +30-6984-460514

Gallery: OSD2019 Highlights

Bigelow Laboratory of Ocean Sciences, USA; University of Southern California, USA

Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), Spain

National University of Ireland Galway (NUIG), Ireland

Video from Spanish TV, featuring OSD and Ibon Cancio from the Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), Spain

Gallery: OSD2018 Highlights

Image of OSD scientists at twighlight Compilations of OSD collecting photos Research divers on a boat

Bigelow Laboratory of Ocean Sciences, USA; Research Marine Centre (CIIMAR), Spain; University of Vigo, Spain

Group of OSD scientists Shot over a small harbour

Faculty of Sciences of Oujda, Morocco; Tvärminne Zoological Station, Finland

Group of OSD scientists R/V Aegaeo

Institute of Marine Biology, Biotechnology and Aquaculture, HCMR (OSD2018-2019 coordinators), Crete, Greece; Sampling at stations OSD5, OSD228 and 229 was performed with the R/V Aegaeo of HCMR

Video from the Facility of Sciences of Oujda, Morocco


  • And this is where it all ends up...OSD2018 sample analysis at IMBBC-HCMR

OSD researchers analysing samples

(a) IMBBC MiSeq Illumina Sequencer that will be used for amplicon sequencing of OSD samples; (b) Thekla Anastasiou, Research Technician at IMBBC-HCMR doing bench work. All OSD samples are being processed by the same person for comparable results; (c) Jon Ben Kristoffersen, Researcher and NGS Technology Expert at IMBBC-HCMR. (photo credit: Paraskevi Polymenakou, IMBBC-HCMR)

Other Information

Registration of New Sites

For the registration of new sites, please contact osd-contact@embrc.eu.

OSD on Social Networks

Follow us on Twitter:

https://twitter.com/ASSEMBLE_Plus #OceanSamplingDay2021


Kopf, A. et al. (2015) The ocean sampling day consortium. GigaScience 4:27 (open access)

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