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.
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Data availability
The global dataset has been deposited in European Nucleotide Archive (ENA) as project PRJEB 39225 (https://www.ebi.ac.uk/ena/browser/view/PRJEB39225), with metadata available on Zenodo (https://zenodo.org/records/6815677).
Code availability
1. Time Analysis software: https://www.illumina.com/search.html?filter=support&q=RTA%20download&p=1.
2. Bcl2fastq Conversion: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
3. Cutadapt, https://github.com/marcelm/cutadapt/releases/tag/v1.18
4. Fastx_clean software, http://www.genoscope.cns.fr/fastxtend
5. FASTX-Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html
6. SortMeRNA v2.1, https://github.com/biocore/sortmerna
7. fastx_estimate_duplicate software, http://www.genoscope.cns.fr/fastxtend
8. fastx_mergepairs software, http://www.genoscope.cns.fr/fastxtend
9. Usearch, https://www.drive5.com/usearch/
10. Trimmomatic: https://github.com/usadellab/Trimmomatic
11. Decontam: https://github.com/benjjneb/decontam
12. Prinseq: https://github.com/uwb-linux/prinseq
13. Qiime2 feature classifier: https://github.com/qiime2/q2-feature-classifier
14. FastQC: https://github.com/s-andrews/FastQC
15. BBTools: https://github.com/kbaseapps/BBTools
16. MultiQC: https://github.com/MultiQC/MultiQC
17. MetaRib: https://github.com/yxxue/MetaRib
18. EMIRGE: https://github.com/csmiller/EMIRGE
19. VSearch: https://github.com/torognes/vsearch
20. 1IDBA_UD: https://github.com/1928d/idba_ud
21. CAP3: https://faculty.sites.iastate.edu/xqhuang/cap3-and-pcap-sequence-and-genome-assemblyprograms
22. eDNAbyss pipeline: https://gitlab.ifremer.fr/abyss-project/
23. MUMU algorithm: https://github.com/frederic-mahe/mumu
24. bbmap: https://sourceforge.net/projects/bbmap/
26. RiboTaxa: https://github.com/oschakoory/RiboTaxa
27. eDNAbyss pipeline(s): https://gitlab.ifremer.fr/abyss-project/),
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Acknowledgements
We express special gratitude to the scientific direction and scientific committee of the “Pourquoi Pas les Abysses?” project and to the board of the French Oceanographic Fleet for allowing unusual use of boat time (including transits) through the AMIGO series and to the mission chiefs of all the crews who kindly sampled for the project. This work was supported by Ifremer during the development of prototypes and protocols in “Pourquoi Pas les Abysses?” and by Genoscope, the Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) and France Génomique (ANR-10-INBS-09) for high-throughput sequencing in eDNAbyss (AP2016–228 France Génomique). We also thank the HADES-ERC Advanced grant (#669947) and the EU Atlas project (678760) and benefited from State aid managed by the National Research Agency under France 2030 for the LIFEDEEPER project (ANR-22-POCE-0007) and the ANR Cerberus (ANR-17-CE02-0003) for samples gathered during the associated cruises and the project MarEEE (MUSE, Montpellier, ANR-16-IDEX-0006) for the improvement of the original bioinformatic pipeline. We warmly acknowledge all the crews, mission chiefs and colleagues who contributed gathering this widespread sampling collection: Covadonga Orejas, Martin Ludvigsen and Eva Ramirez-Llodra, Jean-Paul Justiniano, Yves Fouquet and Ewan Pelleter, Ewen Raugel, Wayne Crawford, Cécile Guieu, Sophie Bonnet, Sophie Arnaud-Haond, François Bonhomme, Pierre-Marie Sarradin, Carlos Duarte, Franck Wenzhoefer, Mathilde Cannat, Norbert Franck, Marie-Anne Cambon, Stéphane Hourdez and Didier Jollivet. We would like gratefully acknowledge the entire Genoscope technical team: Julie Batisse, Odette Beluche, Isabelle Bordelais, Elodie Brun, Maria Dubois, Corinne Dumont, Zineb El Hajji, Barbara Estrada, Thomas Guérin, Chadia Hamon, Sandrine Lebled, Patricia Lenoble and Marine Lepretre, Claudine Louesse, Ghislaine Magdelenat, Eric Mahieu, Claire Milani, Sophie Oztas, Emilie Payen, Emmanuelle Petit, Muriel Ronsin and Benoît Vacherie, for their invaluable work in producing the data. We thank the editorial team and the referees for the improvements suggested to previous versions of this manuscript.
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S.A.H., C.B., J.P., S.C.M. and F.P. wrote the manuscript with the help of F.V., S.H. and M.M. All coauthors reviewed the manuscript. S.A.H., F.P., J.S., C.dV., J.P. and P.W. conceptualized the project. S.A.H. and P.W. obtained funding and administrated the project. B.T., C.L.H., J.A., M.I.B., M.C., S.F., V.C.G., D.J., A.S.L., F.P., J.S., P.M.S., C.S., M.C., A.T.L., S.V., F.B., D.Z., O.U. and J.P., as well as all mission chiefs, contributed to the collection of the environmental samples. B.T., C.L.H., K.A., J.A., M.I.B., F.C., V.C.G., B.G., C.F., S.F., F.L., E.O., G.T.T. and S.A.H. performed the DNA extractions. J.P., C.B., M.I.B. and C.L.H. developed the amplicon sequencing protocol, and S.C.M. and P.P. developed the C.B.H. protocol. J.P., K.L., F.G., P.H.O. and all the Genoscope technical teams were involved in the library preparations and sequencing tasks for metagenomics and metabarcoding, and data curation, S.C.M. and PP for the libraries and sequencing for C.B.H. C.B. and J.M.A. developed Data validation and visualization softwares. S.A.H., B.T., M.V., J.M.A., J.P. and C.B. contributed to Validation. M.I.B., A.C.J., B.G., B.T., L.M., P.D., S.A.H., N.H., K.A., F.V., S.C.M. and P.P. developed the bioinformatics pipelines and/or performed the data analysis. S.P., C.B., S.A.H. and S.V. provided the metadata and data. C.B.H., S.G., J.G., G.S., E.K.J., S.P., S.C.M. and P.D. managed the data to be transmitted to a public repository.
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Arnaud-Haond, S., Trouche, B., Liautard-Haag, C. et al. Omics exploration of deep-sea biodiversity: data from the “Pourquoi Pas les Abysses?” and eDNAbyss projects.
Sci Data (2025). https://doi.org/10.1038/s41597-025-06009-1
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DOI: https://doi.org/10.1038/s41597-025-06009-1
Source: Ecology - nature.com
