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

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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Journal
Scientific Data
Published
2025-12-20
DOI
https://doi.org/10.1038/s41597-025-06009-1
Primary Topic
Environmental DNA in Biodiversity Studies
Type
article
Field-Weighted Citation Impact
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article

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

Pierre Peyret, Frédérique Viard, Stéphane Pesant, Valérie Cueff‐Gauchard et al.
Scientific Data
Environmental DNA in Biodiversity Studies
article

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

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

Abstract

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.

Scientific DataVol. 12(1)
Centre National de la Recherche Scientifique (FR), European Bioinformatics Institute (GB), Ifremer (FR), Université de Bretagne Occidentale (FR), University of Concepción (CL), University of Southern Denmark (DK), Université Clermont Auvergne (FR), Université de Montpellier (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Station Biologique de Roscoff (FR), GEOMAR Helmholtz Centre for Ocean Research Kiel (DE), Sorbonne Université (FR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Ecologie & Evolution (FR), Institut des Sciences de l'Evolution de Montpellier (FR), NORCE Research AS (NO), Genoscope (FR), Adaptation et Diversité en Milieu Marin (FR), CEA Paris-Saclay (FR), Millennium Institute of Oceanography (CL), Observatoire Océanologique de Banyuls-sur-Mer (FR), Marine Biodiversity Exploitation and Conservation (FR), Laboratoire d'Ecogéochimie des Environnements Benthiques (FR), Institut de Recherche pour le Développement (FR)
Flotte Océanographique Française, Agence Nationale de la Recherche
Openalex Percentile: Top 59%
Environmental DNA in Biodiversity Studies
DOIOpen Access PDFOpenAlex
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