First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

Christina Pavloudi¹, Ioulia Santi^{1

2}, Iñigo Azua³, Zuriñe Baña³, Mauro Bastianini⁴, Caroline Belser⁵, Jone Bilbao⁶, Julie Bitz-Thorsen⁷, Caroline Broudin⁸, Mathieu Camusat⁸, Ibon Cancio⁹, Louis Caray-Counil¹⁰, Raffaella Casotti¹¹, Jade Castel⁸, Thierry Comtet¹², Cymon J Cox¹³, Claire Daguin¹², Oihane Díaz de Cerio⁹, Katrina Exter¹⁴, Cécile Fauvelot¹⁵, Miguel J Frada¹⁶, Pierre E Galand¹⁷, Laurence Garczarek¹², Jose González Fernández¹⁸, Laure Guillou¹², Pascal I Hablützel^{14

19}, Hanneloor Heynderickx¹⁴, Céline Houbin⁸, Anne Emmanuelle Kervella¹, Apostolos Krystallas², Rune Lagaisse¹⁴, Arnaud Laroquette¹, Lyvia Lescure¹⁷, Eva Lopes²⁰, Melina Loulakaki², Bruno Louro¹³, Catarina Magalhaes²⁰, Maria Maidanou², Francesca Margiotta²¹, Marina Montresor¹¹, Fabrice Not¹², Estefanía Paredes^{18

22}, Isabella Percopo²¹, Erwan Péru¹⁷, Julie Poulain⁵, Kim Præbel⁷, Fabienne Rigaut-Jalabert⁸, Sarah Romac¹², Melanthia Stavroulaki², Jesús Souza Troncoso^{18

22}, Eric Thiébaut²³, Wilfried Thomas⁸, Andrzej Tkacz¹³, Anna Chiara Trano²¹, Patrick Wincker⁵, Nicolas Pade¹

Affiliations

¹ European Marine Biological Resource Centre (EMBRC-ERIC), Paris, France European Marine Biological Resource Centre (EMBRC-ERIC) Paris France.
² Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) Heraklion Greece.
³ Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU) Biscay Spain.
⁴ CNR-National Research Council, ISMAR - Institute of Marine Sciences, Venice, Italy CNR-National Research Council, ISMAR - Institute of Marine Sciences Venice Italy.
⁵ Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry France.
⁶ Department of Plant Biology and Ecology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain Department of Plant Biology and Ecology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU) Biscay Spain.
⁷ Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway.
⁸ Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, 29680, Roscoff, France Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, 29680 Roscoff France.
⁹ Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU) Biscay Spain.
¹⁰ Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche Villefranche-sur-Mer France.
¹¹ Integrative Marine Ecology Department, Stazione Zoologica Anton Dorn, Naples, Italy Integrative Marine Ecology Department, Stazione Zoologica Anton Dorn Naples Italy.
¹² Sorbonne Université, CNRS, Adaptation et Diversité en Milieu Marin, AD2M, 29680, Roscoff, France Sorbonne Université, CNRS, Adaptation et Diversité en Milieu Marin, AD2M, 29680 Roscoff France.
¹³ Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal Centro de Ciências do Mar, Universidade do Algarve Faro Portugal.
¹⁴ Flanders Marine Institute [Vlaams Instituut voor de Zee (VLIZ)], Ostend, Belgium Flanders Marine Institute [Vlaams Instituut voor de Zee (VLIZ)] Ostend Belgium.
¹⁵ UMR ENTROPIE (IRD, Université de La Réunion, CNRS, IFREMER, Université de la Nouvelle-Calédonie), Villefranche-sur-Mer, France and Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France UMR ENTROPIE (IRD, Université de La Réunion, CNRS, IFREMER, Université de la Nouvelle-Calédonie), Villefranche-sur-Mer, France and Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche Villefranche-sur-Mer France.
¹⁶ Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel and The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel and The Interuniversity Institute for Marine Sciences in Eilat Eilat Israel.
¹⁷ Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls Banyuls sur Mer France.
¹⁸ Centro de Investigación Mariña, Universidade de Vigo, Estación de Ciencias Mariñas de Toralla, Vigo, Spain Centro de Investigación Mariña, Universidade de Vigo, Estación de Ciencias Mariñas de Toralla Vigo Spain.
¹⁹ Vrije Universiteit Brussel, Brussel, Belgium Vrije Universiteit Brussel Brussel Belgium.
²⁰ CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal, Department of Biology, FCUP-Faculty of Sciences of the University of Porto, Porto, Portugal CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal, Department of Biology, FCUP-Faculty of Sciences of the University of Porto Porto Portugal.
²¹ Stazione Zoologica Anton Dohrn, Naples, Italy Stazione Zoologica Anton Dohrn Naples Italy.
²² Department of Ecology and Animal Biology, ECOCOST group, Marine Sciences Faculty, University of Vigo, Vigo, Spain Department of Ecology and Animal Biology, ECOCOST group, Marine Sciences Faculty, University of Vigo Vigo Spain.
²³ Sorbonne Université, CNRS, OSU STAMAR, Station Biologique de Roscoff, 29680, Roscoff, France Sorbonne Université, CNRS, OSU STAMAR, Station Biologique de Roscoff, 29680 Roscoff France.

PMID: 40115125
PMCID: PMC11923592
DOI: 10.3897/BDJ.13.e143585

First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

Christina Pavloudi et al. Biodivers Data J. 2025.

. 2025 Mar 12:13:e143585.

doi: 10.3897/BDJ.13.e143585. eCollection 2025.

Authors

Affiliations

¹ European Marine Biological Resource Centre (EMBRC-ERIC), Paris, France European Marine Biological Resource Centre (EMBRC-ERIC) Paris France.
² Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) Heraklion Greece.
³ Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU) Biscay Spain.
⁴ CNR-National Research Council, ISMAR - Institute of Marine Sciences, Venice, Italy CNR-National Research Council, ISMAR - Institute of Marine Sciences Venice Italy.
⁵ Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry France.
⁶ Department of Plant Biology and Ecology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain Department of Plant Biology and Ecology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU) Biscay Spain.
⁷ Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway.
⁸ Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, 29680, Roscoff, France Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, 29680 Roscoff France.
⁹ Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU) Biscay Spain.
¹⁰ Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche Villefranche-sur-Mer France.
¹¹ Integrative Marine Ecology Department, Stazione Zoologica Anton Dorn, Naples, Italy Integrative Marine Ecology Department, Stazione Zoologica Anton Dorn Naples Italy.
¹² Sorbonne Université, CNRS, Adaptation et Diversité en Milieu Marin, AD2M, 29680, Roscoff, France Sorbonne Université, CNRS, Adaptation et Diversité en Milieu Marin, AD2M, 29680 Roscoff France.
¹³ Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal Centro de Ciências do Mar, Universidade do Algarve Faro Portugal.
¹⁴ Flanders Marine Institute [Vlaams Instituut voor de Zee (VLIZ)], Ostend, Belgium Flanders Marine Institute [Vlaams Instituut voor de Zee (VLIZ)] Ostend Belgium.
¹⁵ UMR ENTROPIE (IRD, Université de La Réunion, CNRS, IFREMER, Université de la Nouvelle-Calédonie), Villefranche-sur-Mer, France and Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France UMR ENTROPIE (IRD, Université de La Réunion, CNRS, IFREMER, Université de la Nouvelle-Calédonie), Villefranche-sur-Mer, France and Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche Villefranche-sur-Mer France.
¹⁶ Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel and The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel and The Interuniversity Institute for Marine Sciences in Eilat Eilat Israel.
¹⁷ Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls Banyuls sur Mer France.
¹⁸ Centro de Investigación Mariña, Universidade de Vigo, Estación de Ciencias Mariñas de Toralla, Vigo, Spain Centro de Investigación Mariña, Universidade de Vigo, Estación de Ciencias Mariñas de Toralla Vigo Spain.
¹⁹ Vrije Universiteit Brussel, Brussel, Belgium Vrije Universiteit Brussel Brussel Belgium.
²⁰ CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal, Department of Biology, FCUP-Faculty of Sciences of the University of Porto, Porto, Portugal CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal, Department of Biology, FCUP-Faculty of Sciences of the University of Porto Porto Portugal.
²¹ Stazione Zoologica Anton Dohrn, Naples, Italy Stazione Zoologica Anton Dohrn Naples Italy.
²² Department of Ecology and Animal Biology, ECOCOST group, Marine Sciences Faculty, University of Vigo, Vigo, Spain Department of Ecology and Animal Biology, ECOCOST group, Marine Sciences Faculty, University of Vigo Vigo Spain.
²³ Sorbonne Université, CNRS, OSU STAMAR, Station Biologique de Roscoff, 29680, Roscoff, France Sorbonne Université, CNRS, OSU STAMAR, Station Biologique de Roscoff, 29680 Roscoff France.

PMID: 40115125
PMCID: PMC11923592
DOI: 10.3897/BDJ.13.e143585

Abstract

The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.

Christina Pavloudi, Ioulia Santi, Iñigo Azua, Zuriñe Baña, Mauro Bastianini, Caroline Belser, Jone Bilbao, Julie Bitz-Thorsen, Caroline Broudin, Mathieu Camusat, Ibon Cancio, Louis Caray-Counil, Raffaella Casotti, Jade Castel, Thierry Comtet, Cymon J Cox, Claire Daguin, Oihane Díaz de Cerio, Katrina Exter, Cécile Fauvelot, Miguel J. Frada, Pierre E Galand, Laurence Garczarek, Jose González Fernández, Laure Guillou, Pascal I. Hablützel, Hanneloor Heynderickx, Céline Houbin, Anne Emmanuelle Kervella, Apostolos Krystallas, Rune Lagaisse, Arnaud Laroquette, Lyvia Lescure, Eva Lopes, Melina Loulakaki, Bruno Louro, Catarina Magalhaes, Maria Maidanou, Francesca Margiotta, Marina Montresor, Fabrice Not, Estefanía Paredes, Isabella Percopo, Erwan Péru, Julie Poulain, Kim Præbel, Fabienne Rigaut-Jalabert, Sarah Romac, Melanthia Stavroulaki, Jesús Souza Troncoso, Eric Thiébaut, Wilfried Thomas, Andrzej Tkacz, Anna Chiara Trano, Patrick Wincker, Nicolas Pade.

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Conflict of interest statement

No conflict of interest to declare Disclaimer: This article is (co-)authored by any of the Editors-in-Chief, Managing Editors or their deputies in this journal.

Figures

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References

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First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

Affiliations

First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

LinkOut - more resources

Full Text Sources