Dataset Information

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

ABSTRACT: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

SUBMITTER: Alberti A

PROVIDER: S-EPMC5538240 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Alberti Adriana A Poulain Julie J Engelen Stefan S Labadie Karine K Romac Sarah S Ferrera Isabel I Albini Guillaume G Aury Jean-Marc JM Belser Caroline C Bertrand Alexis A Cruaud Corinne C Da Silva Corinne C Dossat Carole C Gavory Frédérick F Gas Shahinaz S Guy Julie J Haquelle Maud M Jacoby E'krame E Jaillon Olivier O Lemainque Arnaud A Pelletier Eric E Samson Gaëlle G Wessner Mark M Acinas Silvia G SG Royo-Llonch Marta M Cornejo-Castillo Francisco M FM Logares Ramiro R Fernández-Gómez Beatriz B Bowler Chris C Cochrane Guy G Amid Clara C Hoopen Petra Ten PT De Vargas Colomban C Grimsley Nigel N Desgranges Elodie E Kandels-Lewis Stefanie S Ogata Hiroyuki H Poulton Nicole N Sieracki Michael E ME Stepanauskas Ramunas R Sullivan Matthew B MB Brum Jennifer R JR Duhaime Melissa B MB Poulos Bonnie T BT Hurwitz Bonnie L BL Pesant Stéphane S Karsenti Eric E Wincker Patrick P

Scientific data 20170801

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has ...[more]

PMID: 28763055

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Project description:Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information toward modeling their response to future CO2 levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO2 variability. The current study investigates the interlink between the environmental variability of CO2 and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO2 concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO2 levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.

Dataset Information

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Publications

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

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