Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

• Published in: Cell
• Main Authors: Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, D. B., Christopher M., Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C., Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A., Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels‐Lewis, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Vargas, Colomban de, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Ogata, Hiroyuki, Pesant, Stéphane, Speich, Sabrina, Sullivan, Matthew B., Wincker, Patrick, Sunagawa, Shinichi
• Other Authors: European Commission, Ministerio de Economía y Competitividad (España)
• Format: Article in Journal/Newspaper
• Language: English
• Published: Elsevier 2019
• Subjects: Arctic; Canada; Horten
• Online Access: http://hdl.handle.net/10261/197566; https://doi.org/10.1016/j.cell.2019.10.014

This article is contribution number 94 of Tara Oceans.-- 37 pages, 20 figures, 1 table, supplementary information https://doi.org/10.1016/j.cell.2019.10.014.-- All raw reads are available through ENA at https://www.ebi.ac.uk/ena using the identifiers listed in https://doi.org/10.5281/zenodo.3473199. Processed data are accessible at https://www.ebi.ac.uk/biostudies/studies/S-BSST297, and additional information is provided in https://doi.org/10.5281/zenodo.3473199 and at the companion website: https://www.ocean-microbiome.org. Scripts used in this manuscript are available through a Github repository at https://github.com/SushiLab/omrgc_v2_scripts Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms Tara Oceans (that includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE); European Molecular Biology Laboratory (EMBL); Genoscope/CEA; the French Ministry of Research; the 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); Gordon and Betty Moore Foundation (award 3790); the US National Science Foundation (OCE#1536989 and OCE#1829831 to M.B.S.); the European Union’s Horizon 2020 research and innovation programme (grant agreement 686070); and the Ohio Supercomputer and the EMBL and ETH Zürich HPC facilities for computational support. Funding for the collection and processing of the TARA data set was provided by NASA Ocean Biology and Biogeochemistry program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G, and NNX15AC08G to the University of Maine and Canada Excellence Research Chair on Remote sensing of Canada’s new Arctic frontier Canada Foundation for Innovation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 835067). S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R). S. Sunagawa. is supported by the ETH and the Helmut Horten Foundation and by funding from the Swiss National Foundation (205321_184955) Peer Reviewed