Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects

Sophie Arnaud-Haond; Blandine Trouche; Cathy Liautard-Haag; Karine Alain; Johanne Aubé; François Bonhomme; Miriam I Brandt; Annaëlle Caillarec-Joly; Marie-Anne Cambon; Florence Cornette; Valérie Cueff-Gauchard; Patrick Durand; Colomban de Vargas; Christine Felix; Sandra Fuchs; Babett Günther; Nicolas Henry; Stéphane Hourdez; Didier Jollivet; Anne-Sophie Le Port; Françoise Lesongeur; Loïs Maignien; Sophie Comtet-Marre; Marjolaine Matabos; Emmanuelle Omnes; Pierre Peyret; Florence Pradillon; Jozée Sarrazin; Clemens Schauberger; Adrien Tran Lu Y; Osvaldo Ulloa; Sandrine Vaz; Daniela Zeppili; Frédérique Viard; Frédérick Gavory; Shahinaz Gaz; Julie Guy; E'Krame Jacoby; Pedro H Oliveira; Gaëlle Samson; Jean-Marc Aury; Patrick Wincker; Stéphane Pesant; Julie Poulain; Caroline Belser; Genoscope Technical Team

doi:10.1038/s41597-025-06009-1

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Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects

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Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects

Sophie Arnaud-Haond, Blandine Trouche, Cathy Liautard-Haag, Karine Alain, Johanne Aubé, François Bonhomme, Miriam I Brandt, Annaëlle Caillarec-Joly, Marie-Anne Cambon, Florence Cornette, …

Scientific data, Vol.12(1), pp.1982-23

20/12/2025

DOI: https://doi.org/10.1038/s41597-025-06009-1

PMID: 41422081

Résumé

Biodiversity

DNA Barcoding, Taxonomic

DNA, Environmental

Metagenomics

Oceans and Seas

The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within "Pourquoi Pas les Abysses?" and eDNAbyss projects. Together with information ensuring reproducibility, this dataset -combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization- contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.

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Titre: Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects
Créateurs - sans rôle: Sophie Arnaud-Haond - MARBEC, Univ Montpellier, IFREMER, IRD, CNRS, Sète, France. sophie.arnaud@ifremer.fr
Blandine Trouche - Ifremer
Cathy Liautard-Haag - Ifremer
Karine Alain - Univ Brest, Ifremer, BEEP, F-29280, Plouzané, France
Johanne Aubé - Ifremer
François Bonhomme - ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
Miriam I Brandt - NORCE, Norwegian Research Centre AS, Climate & Environment department, Bergen, Norway
Annaëlle Caillarec-Joly - MARBEC, Univ Montpellier, IFREMER, IRD, CNRS, Sète, France
Marie-Anne Cambon - Univ Brest, Ifremer, BEEP, F-29280, Plouzané, France
Florence Cornette - Ifremer
Valérie Cueff-Gauchard - Ifremer
Patrick Durand - Ifremer
Colomban de Vargas - Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, 3 rue Michel-Ange, Paris, 75016, France
Christine Felix - MARBEC, Univ Montpellier, IFREMER, IRD, CNRS, Sète, France
Sandra Fuchs - Ifremer
Babett Günther - GEOMAR, Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1-3, 24148, Kiel, Germany
Nicolas Henry - CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, Roscoff, 29680, France
Stéphane Hourdez - Laboratoire d'Ecogéochimie des Environnements Benthiques
Didier Jollivet - Station Biologique de Roscoff
Anne-Sophie Le Port - Station Biologique de Roscoff
Françoise Lesongeur - Ifremer
Loïs Maignien - Ifremer
Sophie Comtet-Marre - Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
Marjolaine Matabos - Ifremer
Emmanuelle Omnes - Univ Brest, Ifremer, BEEP, F-29280, Plouzané, France
Pierre Peyret - Université Clermont Auvergne
Florence Pradillon - Ifremer
Jozée Sarrazin - Univ Brest, Ifremer, BEEP, F-29280, Plouzané, France
Clemens Schauberger - University of Southern Denmark
Adrien Tran Lu Y - Ifremer
Osvaldo Ulloa - Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
Sandrine Vaz - Ifremer
Daniela Zeppili - Univ Brest, Ifremer, BEEP, F-29280, Plouzané, France
Frédérique Viard - ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
Frédérick Gavory - Université Paris-Saclay
Shahinaz Gaz - Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, France
Julie Guy - Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, France
E'Krame Jacoby - Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, France
Pedro H Oliveira - Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, France
Gaëlle Samson - Université Paris-Saclay
Jean-Marc Aury - Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
Patrick Wincker - Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
Stéphane Pesant - European Bioinformatics Institute
Julie Poulain - Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. poulain@genoscope.cns.fr
Caroline Belser - Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
Genoscope Technical Team
Détails de publication: Scientific data, Vol.12(1), pp.1982-23
Note de subvention: ANR-22-POCE-0007 / Agence Nationale de la Recherche (French National Research Agency) 678760 / EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council) ANR-10-INBS-09 / Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission) ANR-10-INBS-09 / Agence Nationale de la Recherche (French National Research Agency) 669947 / EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council) ANR-17-CE02-0003 / Agence Nationale de la Recherche (French National Research Agency) ANR-16-IDEX-0006 / Agence Nationale de la Recherche (French National Research Agency)
Identifiants: 99146285609311
Unité académique: MARine Biodiversity, Exploitation & Conservation - MARBEC; Institut des Sciences de l'Evolution - Montpellier - ISEM
Langue: English
Type de ressource: Journal article