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

Type Article
Date 2019-11
Language English
Author(s) Salazar Guillem1, Paoli Lucas1, Alberti Adriana2, 3, Huerta-Cepas Jaime4, 14, Cuenca Miguelangel1, Field Christopher M.1, Coelho Luis Pedro5, 6, 14, Cruaud Corinne3, 7, Engelen Stefan3, 7, Gregory Ann C.8, Labadie Karine3, 7, Marec Claudie9, 10, Pelletier Eric2, 3, Royo-Llonch Marta11, Roux Simon8, Sánchez Pablo11, Uehara Hideya12, 13, Zayed Ahmed A.8, Zeller Georg14, Carmichael Margaux3, 15, Dimier Céline3, 16, 17, Ferland Joannie3, 18, Kandels Stefanie14, Picheral Marc3, 16, Pisarev Sergey19, Poulain Julie2, 3, Acinas Silvia G.11, Babin Marcel18, Bork Peer14, 20, 21, Bowler Chris3, 17, de Vargas Colomban3, 15, Guidi Lionel3, 15, 22, Hingamp Pascal3, 23, Iudicone Daniele24, Karp-Boss Lee25, Karsenti Eric17, 26, Ogata Hiroyuki12, Pesant Stephane27, 28, Speich Sabrina29, Sullivan Matthew B.8, 30, Wincker Patrick2, 3, Sunagawa Shinichi1
Affiliation(s) 1 : Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
2 : Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l’Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
3 : Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
4 : Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain
5 : Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
6 : Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
7 : Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
8 : Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
9 : Département de biologie, Université Laval, QC G1V 0A6, Canada
10 : Laboratoire d’Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
11 : Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
12 : Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
13 : Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
14 : Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
15 : Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
16 : Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
17 : Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
18 : Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
19 : Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
20 : Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany
21 : Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
22 : Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
23 : Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
24 : Stazione Zoologica Anton Dohrn, Naples 80121, Italy
25 : School of Marine Sciences, University of Maine, Orono, ME 04469, USA
26 : Directors’ Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
27 : MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
28 : PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
29 : LMD/IPSL, ENS, PSL Research University, Paris, France
30 : Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA
31 : Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
Source Cell (0092-8674) (Elsevier BV), 2019-11 , Vol. 179 , N. 5 , P. 1068-1083.e21 (38p.)
DOI 10.1016/j.cell.2019.10.014
WOS© Times Cited 58
Abstract 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.
Full Text
File Pages Size Access
Publisher's official version 38 10 MB Open access
Table S1. Pairs of GCs/OGs Linked through Co-expression, Related to STAR Methods. Includes GCs-GCs and GCs-OGs pairs with co-expression Pearson’s r greater than 0.86 (which corresponds to... 850 KB Open access
Document S1. Tara Oceans Coordinators with Affiliations. 2 205 KB Open access
Video Abstract. 132 MB Open access
Top of the page

How to cite 

Salazar Guillem, Paoli Lucas, Alberti Adriana, Huerta-Cepas Jaime, Cuenca Miguelangel, Field 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 Stefanie, Picheral Marc, Pisarev Sergey, Poulain Julie, Acinas Silvia G., Babin Marcel, Bork Peer, Bowler Chris, de Vargas Colomban, Guidi Lionel, Hingamp Pascal, Iudicone Daniele, Karp-Boss Lee, Karsenti Eric, Ogata Hiroyuki, Pesant Stephane, Speich Sabrina, Sullivan Matthew B., Wincker Patrick, Sunagawa Shinichi (2019). Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell, 179(5), 1068-1083.e21 (38p.). Publisher's official version : https://doi.org/10.1016/j.cell.2019.10.014 , Open Access version : https://archimer.ifremer.fr/doc/00591/70339/