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

• Published in: Cell 2019-11, Vol.179 (5), p.1068-1083.e21
• Main Authors: Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, 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, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick
• Format: Article
• Language: English
• Subjects: Biochemistry, Molecular Biology; biogeochemistry; community turnover; eco-systems biology; gene expression change; Gene Expression Regulation; Genomics; Geography; global ocean microbiome; Life Sciences; Metagenome; metatranscriptome; microbial ecology; Microbiota - genetics; Molecular Sequence Annotation; ocean warming; Oceans and Seas; RNA, Messenger - genetics; RNA, Messenger - metabolism; Seawater - microbiology; Tara Oceans; Temperature; Transcriptome - genetics
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2019.10.014

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. [Display omitted] [Display omitted] •A catalog of 47 million genes was generated from 370 globally distributed metagenomes•Meta-omics data integration disentangled the mechanisms of changes in transcript pools•Transcript pool changes of metabolic marker genes show distinct mechanistic patterns•Community turnover as a response to ocean warming may be strongest in polar regions A global survey of gene and transcript collections from ocean microbial communities reveals the differential role of organismal composition and gene expression in the adjustment of ocean microbial communities to environmental change.