Ocean Sampling Day 2020 | Assemble+

Ocean Sampling Day 2020




Event date: 21st June 2020


Map of OSD participant sites since 2014


We are happy to announce that EMBRC infrastructure, through the ASSEMBLE Plus project, supports the call to participate in Ocean Sampling Day 2020, which will take place on 21st June 2020.

Once again the Institute of Marine Biology, Biotechnology and Aquaculture of the Hellenic Center for Marine Research (HCMR) in Heraklion, Crete, will coordinate OSD 2019, supporting all the necessary preparation, documention, and communication. As before, all filters and metadata will be sent to and collected at HCMR for further analysis.

Here follows a short update on where we stand so far:

  1. The shotgun metagenomics data are about to be uploaded to ENA while the metadata to PANGEA and OBIS, accordingly. The sequencing cost has been covered by EMBRC-ERIC, the co-ordinator of ASSEMBLE Plus project. The access links will be sent to you as soon as we get them (end of June or  beginning of July).
  2. OSD will be strengthened thanks to the Horizon 2020-funded AtlantECO project that will kick-off in early 2021 and will support OSD 2022 and 2023, intensifying sampling in Southern Atlantic and including cruises for training the coastal labs on OSD protocols. 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.
  3. 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. In order 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 in aiming to build a European observatory based on the OSD protocols, contributing to global efforts in genomics observation, and establish interactions with other initiatives and communities, such as GSC, GLOMICON and other research infrastructures (e.g. LifeWatch ERIC, e-LTER, ELIXIR). 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
OSD 2020 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:

Brief OSD2020 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 2020 (OSD2020) 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 OSD2020 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 2020 

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 #OceanSamplingDay2020


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

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