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A la portada: Institut de Ciències del Mar, (English) There is a myriad of microorganisms on Earth contributing to global biogeochemical cycles. In the surface ocean, the smallest microbes (picoplankton) are responsible for an important fraction of the total atmospheric carbon and nitrogen fixation. The ocean picoplankton encompasses both prokaryotes (bacteria and archaea) and tiny unicellular eukaryotes (protists). Despite their overall importance for the functioning of the biosphere, many questions remain unanswered on their biogeography, population dynamics, interactions, and evolution. Answering these questions is essential in the context of global change, as alterations of the ocean microbiome could impact the function of multiple ecosystems. In this thesis, we aim at reducing the knowledge gap on the above topics through the application of High-Throughput Sequencing (HTS) and genomic approaches, using data collected during the circumglobal Tara Oceans and Malaspina-2010 expeditions, as well as at the Gulf of Maine (North Atlantic), and two Northwestern Mediterranean coastal microbial observatories (BBMO and SOLA stations). Chapters 1 and 2 are dedicated to a small protistan group of heterotrophic flagellates (HF): the Marine Stramenopiles (MAST)-4, relevant during picoplankton grazing and nutrient remineralization. Due to its widespread distribution and relatively high abundance, MAST-4 has become a target group of microbes to study HF. Unfortunately, MAST-4 remains uncultured. We investigated four evolutionary-related species of MAST-4 (species A, B, C, and E) by reconstructing their genomes with Single-Cell genomics data. In chapter 1, co-occurrence and biogeographic analyses in the surface global ocean indicated contrasting patterns driven by temperature. Although MAST-4 species were similar in terms of broad metabolic functions, they differed in the set of genes related to the food degradation machinery. We proposed that differential niche adaptation to temperature and prey type has promoted the evo, (Español) Existen un sinfín de microorganismos que contribuyen a los ciclos biogeoquímicos globales. En la superficie oceánica, los microbios más pequeños (picoplancton) son responsables de fijar una gran parte del total de carbono y nitrógeno terrestre. El picoplancton agrupa tanto a procariotas (bacterias y arqueas) como a pequeños eucariotas unicelulares (protistas). A pesar de su importancia en el funcionamiento de la biosfera, existen aún muchas preguntas sin respuesta relacionadas con su biogeografía, dinámica poblacional, interacciones, y evolución. Responder dichas preguntas es esencial en el contexto del cambio climático, ya que alteraciones en la microbiota marina podría impactar en el funcionamiento de múltiples ecosistemas. El principal objetivo de la tesis es llenar el vacío existente sobre los temas mencionados a través de la aplicación de técnicas de secuenciación de alto rendimiento (HTS) y de métodos genómicos, usando datos recolectados durante las expediciones globales de Tara Oceans y Malaspina-2010, el Golfo de Maine (Océano Atlántico Norte), y dos observatorios situados en la costa noroeste del mar Mediterráneo (BBMO y SOLA). Los capítulos 1 y 2 están dedicados a un grupo de pequeños protistas flagelados heterótrofos (HF): los Stramenopilos Marinos (MAST)-4, relevantes en el consumo de picoplancton y la re-mineralización de nutrientes. Debido a su distribución generalizada y su abundancia relativa elevada, MAST-4 se ha convertido en un grupo microbiano modelo para estudiar a los HF. Hemos reconstruido los genomas de cuatro especies relacionadas evolutivamente de MAST-4 (A, B, C, y E) usando datos de genómica de célula única (SCG). En el capítulo 1, los análisis de coocurrencia y biogeografía en la superficie oceánica global indicaron patrones contrastantes relacionados con la temperatura. Aunque las especies de MAST-4 compartían funciones metabólicas, su contenido genético relacionado con la degradación de comida era diferente. Por lo tanto, pro, Postprint (published version)

Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs., Postprint (published version)