Patterns and drivers of diatom diversity and abundance in the global ocean

This article is contribution number 156 of Tara Oceans.-- 21 pages, 9 figures, supplementary information https://doi.org/10.1038/s41467-025-58027-7.-- Data availability: The authors declare that all the data supporting the findings of this study are publicly available in the following repositories a...

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Authors: Pierella Karlusich, Juan J., Cosnier, Karen, Zinger, Lucie, Henry, Nicolas, Nef, Charlotte, Bernard, Guillaume, Scalco, Eleonora, Dvorak, Etienne, Tara Oceans Coordinators, Acinas, Silvia G., Rocha Jimenez Vieira, Fabio, Delage, Erwan, Chaffron, Samuel, Ovchinnikov, Sergey, Zingone, Adriana, Bowler, Chris
Format: article
Status:Published version
Publication Date:2025
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/389464
Online Access:http://hdl.handle.net/10261/389464
Access Level:Open access
Keyword:http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
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dc.title.none.fl_str_mv Patterns and drivers of diatom diversity and abundance in the global ocean
title Patterns and drivers of diatom diversity and abundance in the global ocean
spellingShingle Patterns and drivers of diatom diversity and abundance in the global ocean
Pierella Karlusich, Juan J.
http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
title_short Patterns and drivers of diatom diversity and abundance in the global ocean
title_full Patterns and drivers of diatom diversity and abundance in the global ocean
title_fullStr Patterns and drivers of diatom diversity and abundance in the global ocean
title_full_unstemmed Patterns and drivers of diatom diversity and abundance in the global ocean
title_sort Patterns and drivers of diatom diversity and abundance in the global ocean
dc.creator.none.fl_str_mv Pierella Karlusich, Juan J.
Cosnier, Karen
Zinger, Lucie
Henry, Nicolas
Nef, Charlotte
Bernard, Guillaume
Scalco, Eleonora
Dvorak, Etienne
Tara Oceans Coordinators
Acinas, Silvia G.
Rocha Jimenez Vieira, Fabio
Delage, Erwan
Chaffron, Samuel
Ovchinnikov, Sergey
Zingone, Adriana
Bowler, Chris
author Pierella Karlusich, Juan J.
author_facet Pierella Karlusich, Juan J.
Cosnier, Karen
Zinger, Lucie
Henry, Nicolas
Nef, Charlotte
Bernard, Guillaume
Scalco, Eleonora
Dvorak, Etienne
Tara Oceans Coordinators
Acinas, Silvia G.
Rocha Jimenez Vieira, Fabio
Delage, Erwan
Chaffron, Samuel
Ovchinnikov, Sergey
Zingone, Adriana
Bowler, Chris
author_role author
author2 Cosnier, Karen
Zinger, Lucie
Henry, Nicolas
Nef, Charlotte
Bernard, Guillaume
Scalco, Eleonora
Dvorak, Etienne
Tara Oceans Coordinators
Acinas, Silvia G.
Rocha Jimenez Vieira, Fabio
Delage, Erwan
Chaffron, Samuel
Ovchinnikov, Sergey
Zingone, Adriana
Bowler, Chris
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Agence Nationale de la Recherche (France)
Fondation BNP Paribas
Fonds Français pour l'Environnement Mondial
Simons Foundation
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
topic http://metadata.un.org/sdg/14
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
description This article is contribution number 156 of Tara Oceans.-- 21 pages, 9 figures, supplementary information https://doi.org/10.1038/s41467-025-58027-7.-- Data availability: The authors declare that all the data supporting the findings of this study are publicly available in the following repositories and in the supplementary information files of this paper. The contextual data are available in Pangaea (www.pangaea.de) with the identifier https://doi.org/10.1594/PANGAEA.875582, and a simplified version is available in https://zenodo.org/records/7229815. rDNA 18S metabarcoding data are deposited at the European Nucleotide Archive under accession numbers PRJEB6610 and PRJEB9737, and metagenomic and metatranscriptomic data under PRJEB402, PRJEB9691, PRJEB9738 and PRJEB9739. The ASV table and the taxonomic annotation for the V4 marker are available in https://zenodo.org/records/13881376 and for the V9 marker in https://zenodo.org/records/13881418. The files for the Marine Atlas of Tara Oceans Unigenes version 1.5 (MATOU-v1.5) are available in https://www.genoscope.cns.fr/tara/#MATOU-1.5, including the FASTA sequences, taxonomic and functional annotation tables, as well as metagenomic and metatranscriptomic abundance tables. The manually curated MAGs by Delmont et al.72 are available at https://www.genoscope.cns.fr/tara/#SMAGs. Flow cytometry data are available at https://data.mendeley.com/datasets/p9r9wttjkm/2. Source data are provided in this paper.-- Code availability: Scripts producing the ASV tables are publicly available here: https://gitlab.univ-nantes.fr/combi-ls2n/taradada. The scripts for the ASV taxonomic assignment are publicly available here: https://gitlab.sb-roscoff.fr/nhenry/abims-metabarcoding-taxonomic-assignment/-/tree/v1.0.1. Scripts for producing the figures in this paper are in https://github.com/JJPierellaKarlusich/Diatom_patters/tree/main (Pierella Karlusich, JJ, Patterns and drivers of diatom diversity and abundance in the global ocean, Zenodo, https://doi.org/10.5281/zenodo.14890007, 2025)
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
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dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/389464
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spelling Patterns and drivers of diatom diversity and abundance in the global oceanPierella Karlusich, Juan J.Cosnier, KarenZinger, LucieHenry, NicolasNef, CharlotteBernard, GuillaumeScalco, EleonoraDvorak, EtienneTara Oceans CoordinatorsAcinas, Silvia G.Rocha Jimenez Vieira, FabioDelage, ErwanChaffron, SamuelOvchinnikov, SergeyZingone, AdrianaBowler, Chrishttp://metadata.un.org/sdg/14Conserve and sustainably use the oceans, seas and marine resources for sustainable developmentThis article is contribution number 156 of Tara Oceans.-- 21 pages, 9 figures, supplementary information https://doi.org/10.1038/s41467-025-58027-7.-- Data availability: The authors declare that all the data supporting the findings of this study are publicly available in the following repositories and in the supplementary information files of this paper. The contextual data are available in Pangaea (www.pangaea.de) with the identifier https://doi.org/10.1594/PANGAEA.875582, and a simplified version is available in https://zenodo.org/records/7229815. rDNA 18S metabarcoding data are deposited at the European Nucleotide Archive under accession numbers PRJEB6610 and PRJEB9737, and metagenomic and metatranscriptomic data under PRJEB402, PRJEB9691, PRJEB9738 and PRJEB9739. The ASV table and the taxonomic annotation for the V4 marker are available in https://zenodo.org/records/13881376 and for the V9 marker in https://zenodo.org/records/13881418. The files for the Marine Atlas of Tara Oceans Unigenes version 1.5 (MATOU-v1.5) are available in https://www.genoscope.cns.fr/tara/#MATOU-1.5, including the FASTA sequences, taxonomic and functional annotation tables, as well as metagenomic and metatranscriptomic abundance tables. The manually curated MAGs by Delmont et al.72 are available at https://www.genoscope.cns.fr/tara/#SMAGs. Flow cytometry data are available at https://data.mendeley.com/datasets/p9r9wttjkm/2. Source data are provided in this paper.-- Code availability: Scripts producing the ASV tables are publicly available here: https://gitlab.univ-nantes.fr/combi-ls2n/taradada. The scripts for the ASV taxonomic assignment are publicly available here: https://gitlab.sb-roscoff.fr/nhenry/abims-metabarcoding-taxonomic-assignment/-/tree/v1.0.1. Scripts for producing the figures in this paper are in https://github.com/JJPierellaKarlusich/Diatom_patters/tree/main (Pierella Karlusich, JJ, Patterns and drivers of diatom diversity and abundance in the global ocean, Zenodo, https://doi.org/10.5281/zenodo.14890007, 2025)Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity is confirmed, and the most prevalent genera are Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We define 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection are among the cellular functions in which natural diatom populations invest the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impactsThis work was granted access to the HPC resources of IDRIS, Jean Zay supercomputer, under the allocation 2020–DARI A0080111497 made by GENCI, and has been supported by the FFEM - French Facility for Global Environment, French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). C.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Diatomic; grant agreement No. 835067), the Horizon Europe projects Marco-Bolo (grant agreement no. 101082021) and BlueRemediomics (grant agreement no. 101082304), Agence Nationale de la Recherche “Phytomet” (ANR-16-CE01-0008) and BrownCut (ANR-19-CE20-0020), and the BNP Paribas Foundation Climate & Biodiversity Initiative. J.J.P.K. acknowledges postdoctoral funding from the Fonds Français pour l’Environnement Mondial and by Moore–Simons Project on the Origin of the Eukaryotic Cell, Simons Foundation (735929LPI)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewedNature Publishing GroupEuropean CommissionAgence Nationale de la Recherche (France)Fondation BNP ParibasFonds Français pour l'Environnement MondialSimons FoundationAgencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/389464reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/835067info:eu-repo/grantAgreement/EC/HE/101082021info:eu-repo/grantAgreement/EC/HE/101082304https://doi.org/10.1038/s41467-025-58027-7Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3894642026-05-22T06:33:51Z
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