Biodiversity Literature Repository

Submit to community
Liberated Data
Published January 22, 2026 | Version v1
Journal article Open

Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2)

Authors/Creators

  • 1. European Marine Biological Resource Centre (EMBRC-ERIC), Paris, France|Hellenic Center for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Greece
  • 2. European Marine Biological Resource Centre (EMBRC-ERIC), Paris, France
  • 3. Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
  • 4. Plentzia Marine Station (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Spain|Department of Immunology, Microbiology & Parasitology, University of the Basque Country (UPV/EHU), Plentzia, Spain
  • 5. Department of Immunology, Microbiology & Parasitology, University of the Basque Country (UPV/EHU), Plentzia, Spain|Plentzia Marine Station (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Spain
  • 6. Institute of Marine Sciences (ISMAR) National Research Council of Italy (CNR), Venice, Italy
  • 7. Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
  • 8. Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
  • 9. Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Plentzia, Spain|Plentzia Marine Station (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Spain
  • 10. The Marine Biological Association, Plymouth, United Kingdom
  • 11. Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, 29680 Roscoff, France
  • 12. CBET+ Research Group, Department of Zoology & Animal Cell Biology, University of the Basque Country (UPV/EHU), Biscay, Spain|Plentzia Marine Station (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Spain
  • 13. Sorbonne Université, CNRS, Laboratoire Océanographique de Villefranche-sur-mer, Villefranche sur mer, France
  • 14. Sorbonne Université, CNRS, UMR7144 AD2M, Station Biologique de Roscoff, 29680 Roscoff, France
  • 15. Centro de Ciências do Mar do Algarve (CCMAR/CIMAR LA), Universidade do Algarve, Faro, Portugal
  • 16. School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom|The Marine Biological Association, Plymouth, United Kingdom
  • 17. Flanders Marine Institute (VLIZ), Ostend, Belgium
  • 18. Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
  • 19. Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Banyuls sur Mer, France
  • 20. Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
  • 21. Faculty of Sciences of University of Porto, Porto, Portugal|Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Matosinhos, Portugal
  • 22. Hellenic Center for Marine Research (HCMR), Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Heraklion, Greece
  • 23. Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
  • 24. Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France|Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
  • 25. Sorbonne Université, CNRS, OSU STAMAR, Station Biologique de Roscoff, 29680 Roscoff, France

Description

The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.

Files

BDJ_article_178484.pdf

Files (759.3 kB)

Name Size Download all
md5:abba67b692dfd57077c82b76ea52036a
524.4 kB Preview Download
md5:687d86588fa943941f07d8f7dbc28ae9
234.9 kB Preview Download

Linked records

Additional details

Cites
Publication: 10.1038/sdata.2017.93 (DOI)
Publication: 10.1111/mec.15472 (DOI)
Publication: 10.1093/nar/gkab1046 (DOI)
Publication: 10.1111/1755-0998.14073 (DOI)
Publication: 10.1093/bioinformatics/btn025 (DOI)
Publication: 10.1093/nar/gkae975 (DOI)
Publication: 10.3897/arphapreprints.e149221 (DOI)
Publication: 10.3897/bdj.13.e143585 (DOI)
Publication: 10.1016/j.scitotenv.2021.151783 (DOI)
Publication: 10.25607/OBP-1653 (DOI)
Publication: 10.3389/fmars.2023.1118120 (DOI)
Publication: 10.1641/b570707 (DOI)
Publication: 10.1016/j.tig.2023.01.005 (DOI)
Has part
Figure: 10.3897/BDJ.14.e178484.figure1 (DOI)
Other: 10.3897/BDJ.14.e178484.suppl1 (DOI)

References

  • Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury J, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Bazire P, Beluche O, Bertrand L, Besnard-Gonnet M, Bordelais I, Boutard M, Dubois M, Dumont C, Ettedgui E, Fernandez P, Garcia E, Aiach NG, Guerin T, Hamon C, Brun E, Lebled S, Lenoble P, Louesse C, Mahieu E, Mairey B, Martins N, Megret C, Milani C, Muanga J, Orvain C, Payen E, Perroud P, Petit E, Robert D, Ronsin M, Vacherie B, Acinas S, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki M, Stepanauskas R, Sullivan M, Brum J, Duhaime M, Poulos B, Hurwitz B, Acinas S, Bork P, Boss E, Bowler C, De Vargas C, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Raes J, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan M, Sunagawa S, Wincker P, Pesant S, Karsenti E, Wincker P (2017) Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data 4 (1). https://doi.org/10.1038/sdata.2017.93
  • Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan D, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A (2020) Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Molecular Ecology 30 (13): 2937‑2958. https://doi.org/10.1111/mec.15472
  • Courtot M, Gupta D, Liyanage I, Xu F, Burdett T (2021) BioSamples database: FAIRer samples metadata to accelerate research data management. Nucleic Acids Research 50 https://doi.org/10.1093/nar/gkab1046
  • Daraghmeh N, Exter K, Pagnier J, Balazy P, Cancio I, Chatzigeorgiou G, Chatzinikolaou E, Chelchowski M, Chrismas NAM, Comtet T, Dailianis T, Deneudt K, Diaz de Cerio O, Digenis M, Gerovasileiou V, González J, Kauppi L, Kristoffersen JB, Kukliński P, Lasota R, Levy L, Małachowicz M, Mavrič B, Mortelmans J, Paredes E, Poćwierz‐Kotus A, Reiss H, Santi I, Sarafidou G, Skouradakis G, Solbakken J, Staehr PU, Tajadura J, Thyrring J, Troncoso J, Vernadou E, Viard F, Zafeiropoulos H, Zbawicka M, Pavloudi C, Obst M (2025) A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program <scp>ARMS</scp>‐<scp>MBON</scp> 2018–2020. Molecular Ecology Resources 25 (4). https://doi.org/10.1111/1755-0998.14073
  • Flanders Marine Institute (2025) MarineRegions.org. www.marineregions.org. Accessed on: 2025-10-22.
  • Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24 (5): 713‑714. https://doi.org/10.1093/bioinformatics/btn025
  • O'Cathail C, Ahamed A, Burgin J, Cummins C, Devaraj R, Gueye K, Gupta D, Gupta V, Haseeb M, Ihsan M, Ivanov E, Jayathilaka S, Kadhirvelu V, Kumar M, Lathi A, Leinonen R, McKinnon J, Meszaros L, Pauperio J, Pesant S, Rahman N, Rinck G, Selvakumar S, Suman S, Sunthornyotin Y, Ventouratou M, Waheed Z, Woollard P, Yuan D, Zyoud A, Burdett T, Cochrane G (2024) The European Nucleotide Archive in 2024. Nucleic Acids Research 53 https://doi.org/10.1093/nar/gkae975
  • Pagnier J, Allcock L, Cancio I, Chatzinikolaou E, Chatzigeorgiou G, Chrismas N, Costantini F, Dailianis T, Deneudt K, Díaz de Cerio O, Digenis M, Exter K, Gerovasileiou V, González Fernández J, Kauppi L, Keklikoglou K, Kristoffersen JB, Lagaisse R, Mavrič B, Mortelmans J, Paredes E, Pavloudi C, Piazza A, Power AM, Ramšak A, Santi I, Solbakken J, Stavroulaki M, Stæhr P, Tajadura J, Souza Troncoso J, Vasileiadou K, Vernadou E, Obst M (2025) A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2020-2021. ARPHA Preprints https://doi.org/10.3897/arphapreprints.e149221
  • Pavloudi C, Santi I, Azua I, Baña Z, Bastianini M, Belser C, Bilbao J, Bitz-Thorsen J, Broudin C, Camusat M, Cancio I, Caray-Counil L, Casotti R, Castel J, Comtet T, Cox C, Daguin C, Díaz de Cerio O, Exter K, Fauvelot C, Frada M, Galand P, Garczarek L, González Fernández J, Guillou L, Hablützel P, Heynderickx H, Houbin C, Kervella A, Krystallas A, Lagaisse R, Laroquette A, Lescure L, Lopes E, Loulakaki M, Louro B, Magalhaes C, Maidanou M, Margiotta F, Montresor M, Not F, Paredes E, Percopo I, Péru E, Poulain J, Præbel K, Rigaut-Jalabert F, Romac S, Stavroulaki M, Souza Troncoso J, Thiébaut E, Thomas W, Tkacz A, Trano AC, Wincker P, Pade N (2025) First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples. Biodiversity Data Journal 13 https://doi.org/10.3897/bdj.13.e143585
  • Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJ, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S (2022) Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Science of The Total Environment 818 https://doi.org/10.1016/j.scitotenv.2021.151783
  • Santi I, Casotti R, Comtet T, Cunliffe M, Koulouri Y, Macheriotou L, Not F, Obst M, Pavloudi C, Romac S, Thiebaut E, Vanaverbeke J, Pade N (2021) European Marine Omics Biodiversity Observation Network (EMO BON) Handbook. EMBRC-ERIC. https://doi.org/10.25607/OBP-1653
  • Santi I, Beluche O, Beraud M, Buttigieg PL, Casotti R, Cox C, Cunliffe M, Davies N, de Cerio OD, Exter K, Kervella AE, Kotoulas G, Lagaisse R, Laroquette A, Louro B, Not F, Obst M, Pavloudi C, Poulain J, Præbel K, Vanaverbeke J, Pade N (2023) European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation. Frontiers in Marine Science 10 https://doi.org/10.3389/fmars.2023.1118120
  • Spalding M, Fox H, Allen G, Davidson N, Ferdaña Z, Finlayson M, Halpern B, Jorge M, Lombana A, Lourie S, Martin K, McManus E, Molnar J, Recchia C, Robertson J (2007) Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas. BioScience 57 (7): 573‑583. https://doi.org/10.1641/b570707
  • Theissinger K, Fernandes C, Formenti G, Bista I, Berg P, Bleidorn C, Bombarely A, Crottini A, Gallo G, Godoy J, Jentoft S, Malukiewicz J, Mouton A, Oomen R, Paez S, Palsbøll P, Pampoulie C, Ruiz-López M, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel A, Zhang G, Jarvis E, Bálint M, Ciofi C, Waterhouse R, Mazzoni C, Höglund J, Aghayan S, Alioto T, Almudi I, Alvarez N, Alves P, Amorim do Rosario I, Antunes A, Arribas P, Baldrian P, Bertorelle G, Böhne A, Bonisoli-Alquati A, Boštjančić L, Boussau B, Breton C, Buzan E, Campos P, Carreras C, Castro LFC, Chueca L, Čiampor F, Conti E, Cook-Deegan R, Croll D, Cunha M, Delsuc F, Dennis A, Dimitrov D, Faria R, Favre A, Fedrigo O, Fernández R, Ficetola GF, Flot J, Gabaldón T, Agius D, Giani A, Gilbert MTP, Grebenc T, Guschanski K, Guyot R, Hausdorf B, Hawlitschek O, Heintzman P, Heinze B, Hiller M, Husemann M, Iannucci A, Irisarri I, Jakobsen K, Klinga P, Kloch A, Kratochwil C, Kusche H, Layton KS, Leonard J, Lerat E, Liti G, Manousaki T, Marques-Bonet T, Matos-Maraví P, Matschiner M, Maumus F, Mc Cartney A, Meiri S, Melo-Ferreira J, Mengual X, Monaghan M, Montagna M, Mysłajek R, Neiber M, Nicolas V, Novo M, Ozretić P, Palero F, Pârvulescu L, Pascual M, Paulo O, Pavlek M, Pegueroles C, Pellissier L, Pesole G, Primmer C, Riesgo A, Rüber L, Rubolini D, Salvi D, Seehausen O, Seidel M, Studer B, Theodoridis S, Thines M, Urban L, Vasemägi A, Vella A, Vella N, Vernes S, Vernesi C, Vieites D, Wheat C, Wörheide G, Wurm Y, Zammit G (2023) How genomics can help biodiversity conservation. Trends in Genetics 39 (7): 545‑559. https://doi.org/10.1016/j.tig.2023.01.005