[EN] Primary production is the synthesis of organic matter out of inorganic molecules, and in most ecosystems is achieved through photosynthesis. Eukaryotic microbial phototrophs and mixotrophs are main contributors to primary production in the global oligotrophic ocean, supporting processes of energy and biomass trophic transfer at a planetary scale. Despite the ecological value of these organisms, their wide taxonomic and functional diversity remains largely unknown. In this thesis, we use different types of molecular data obtained from the Tara Oceans circumglobal expedition to assess the composition and trophic diversity of picoeukaryotic primary producers in the oligotrophic ocean. In the first part of the thesis, we compare metagenomic and metabarcoding data to assess the evolutionary diversity and relative abundance of picophototrophic organisms. We identified phototrophic bacteria as three-fold more abundant and significantly less phylogenetically diverse than phototrophic picoeukayrotes. Prymnesiophyceae, Mamiellophyceae, Pelagophyceae and Dictiochophyceae appeared as the dominant groups of phototrophic picoeukaryotes in terms of relative richness and abundance. In the fourth chapter, we describe a predictive model to quantify the abundance of trophic groups in metagenomic samples. This taxonomy-free approach revealed the dominance of photo-trophic organisms across all ocean basins, while the contribution of phagomixo- and phago-trophs oscillated around 25% of the relative abundance in most samples. In the last study included in this thesis we assess the distribution of a collection of single-cell amplified genomes across all Tara Oceans samples. Our results argue that single-cell sequencing technique has the potential to recover the genome of dominant protists in the global oligotrophic ocean with a relatively low sampling effort. Overall, this work describes a number of approaches based on molecular data for the assessment of primary producers distribution and diversity in marine environments

[FR] La production primaire est la synthèse de matière organique à partir de molécules inorganiques et, dans la plupart des écosystèmes, elle est réalisée à travers de la photosynthèse. Les microbiens eucaryotes phototrophes et mixotrophes sont les principaux contributeurs à la production primaire dans l’océan oligotrophe global, soutenant les processus de transfert trophique d’énergie et de biomasse à l’échelle planétaire. [...]

Memoria de tesis doctoral presentada por Laura Rubinat Ripoll para obtener el título de Docteur en la Spécialité Écologie por la Sorbonne Université, realizada bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC), del Dr. Colomban de Vargas y el Dr. Olivier Jaillon.-- 181 pages, figures, tables