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Since 2004, the Service facility SNAPO-CO2 (Service National d’Analyse des Paramètres Océaniques du CO2) housed by the LOCEAN laboratory (Paris, France) has been in charge for the analysis of Total Alkalinity (AT) and Total dissolved inorganic carbon (CT) of seawater samples on a series of cruises or ships of opportunity conducted in different regions in the frame of French projects. More than 44000 observations are synthetized in this work. Sampling was performed either from CTD-Rosette casts (Niskin bottles) or collected from the ship’s seawater supply (intake at about 5m depth). After completion of each cruise, discrete samples were returned back at LOCEAN laboratory and stored in a dark room at 4 °C before analysis generally within 2-3 months after sampling (sometimes within a week). AT and CT were analyzed simultaneously by potentiometric titration using a closed cell (Edmond, 1970). Certified Reference Materials (CRMs) provided by Pr. A. Dickson (Scripps Institution of Oceanography, San Diego, USA) were used to calibrate the measurements. The same instrumentation was used for underway measurements during OISO cruises (https://doi.org/10.18142/228) and OISO AT-CT data for 1998-2018 in the South Indian Ocean added in this synthesis. The synthesis is organized in two files (one for Global ocean and the Coastal Zones, one for the Mediterranean Sea) with the same format: Cruise name, Ship name, day, month, year, hour, minute, second, latitude, longitude, depth, AT (µmol/kg), Flag-AT, CT (µmol/kg), Flag-CT, Temperature (°C), Flag-Temp, Salinity (PSU), Flag-Salinity, nsample/cruise, nsample on file, sampling method.

Abstract Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a . The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses.

Marine plankton mitigate anthropogenic greenhouse gases, modulate biogeochemical cycles, and provide fishery resources. Plankton is distributed across a stratified ecosystem of sunlit surface waters and a vast, though understudied, mesopelagic ‘dark ocean’. In this study, we mapped viruses, prokaryotes, and pico-eukaryotes across 32 globally-distributed cross-depth samples collected during the Tara Oceans Expedition, and assessed their ecologies. Based on depth and O 2 measurements, we divided the marine habitat into epipelagic, oxic mesopelagic, and oxygen minimum zone (OMZ) eco-regions. We identified specific communities associated with each marine habitat, and pinpoint environmental drivers of dark ocean communities. Our results indicate that water masses primarily control mesopelagic community composition. Through co-occurrence network inference and analysis, we identified signature communities strongly associated with OMZ eco-regions. Mesopelagic communities appear to be constrained by a combination of factors compared to epipelagic communities. Thus, variations in a given abiotic factor may cause different responses in sunlit and dark ocean communities. This study expands our knowledge about the ecology of planktonic organisms inhabiting the mesopelagic zone.

Abstract Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatom Phaeodactylum triconrnutum ( Pt ) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identified Pt NCDs using metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We demonstrated nitrogen fixation in Pt NCDs and their close genetic affiliation with NCDs from the environment. We showed the wide occurrence of this type of symbiosis with the isolation of NCDs from other microalgae and their identification in the environment and in co-occurrence with photosynthetic microalgae. Overall, this study provides evidence for a previously overlooked symbiosis using a multidisciplinary model-based approach which will consequently help understand the different players driving global marine nitrogen fixation.

At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.

In the last few decades, novel approaches have been applied to the study of marine microorganism aiming to retrieve taxa that escape isolation in culture. Culture independent methodologies, together with high-throughput sequencing and oceanographic samplings, have provided insight into a previously unknown taxonomic and functional diversity of marine microorganisms. Marine microorganisms play a fundamental role in nutrient cycling and climate regulation at a planetary scale. Thus, it is of paramount importance to define their taxonomic classification, distribution, habitat preferences and functional properties in the ocean. Linking taxonomy with function has been a challenge in Microbial Ecology, and in the recent years two alternatives have been developed towards this end. Single Cell Genomics allows the sequencing of individual genomes from environmental samples (Single Amplified Genomes, SAGs) and genome reconstruction from metagenomes allows building genomes from the community's DNA content (Metagenomic Assembled Genomes, MAGs). In the present dissertation, I have retrieved SAGs and MAGs from underexplored areas like the North Indian Ocean and the Arctic Ocean. The North Indian Ocean is subject to seasonal upwellings that provide surface waters with fresh nutrients, resulting in phytoplankton blooms. Such high primary productivity in the surface waters results in heterotrophic metabolism in the subsurface, by prokaryotes that feed on the products released by primary producers. Such high heterotrophic activity consumes the available oxygen, and together with physical processes than prevent water mixing, generates an oxygen-depleted layer in the water column: the Oxygen Minimum Zone. These water layers are predicted to increase due to global warming and have caught the attention of microbial ecologists as they are rich in microbes involved in the cycling of nitrogen and several microaerophilic and anaerobic metabolisms. Even though the North Indian Ocean has one of the most intense and large OMZs, little is known about the prokaryotic diversity of this environment. With Single Cell Genomics I was able to retrieve 98 SAGs of a novel species in the genus Kordia and after genetically screening them for microdiversity patterns, ten were selected for complete sequencing. The ten genomes were co-assembled together and manually curated for the generation of a reference, almost complete, draft genome. I described the novelty of this species based on multiple phylogenies and comparative genomics with the other described species of the genus Kordia. I also defined the functional potential and niche preference of the novel species combining its functional annotation with its distribution in the different metagenomes of the water column of origin, that included multiple depths and size fractions. The Arctic Ocean has a huge impact in climate regulation of our Planet and is currently being affected severely by global warming. The prokaryotic diversity of its waters has been assessed in sporadic sampling events, mostly focused on a specific season or geographic extension. In the present work I have built 3550 bins from Arctic metagenomes from different regions and seasons that are representative of almost half of the genetic content of the community. Of these, 530 can be classified as MAGs due to their medium and high-quality features and include a majority of novel taxa, especially at the species level but also at higher taxonomic ranks like Class in the case of Bacteria. I have studied their implications for the Arctic's carbon cycle, their distribution patterns and habitat preferences, and have defined habitat generalists and specialists that can serve as future sentinels of climate change in the Arctic. Overall, this dissertation provides new insights into the taxonomic and functional diversity of uncultured taxa, and proposes new methodologies to improve genome assembly and quality controls in meta-omic mappings En las últimas décadas se han aplicado nuevas metodologías al estudio de los microorganismos marinos para recuperar taxones que no crecen en cultivo. La combinación de técnicas independientes de cultivo, secuenciación masiva y muestreos oceanográficos a gran escala han permitido explorar la diversidad taxonómica y funcional microbiana a un nivel de resolución previamente desconocido. Los microorganismos marinos juegan un papel fundamental en los ciclos biogeoquímicos y regulación del clima a escala planetaria. Por eso es importante que definamos su taxonomía, distribución, hábitats y propiedades funcionales en el océano. Relacionar la taxonomía con la función a nivel genómico ha sido un reto en la ecología microbiana, pero en los últimos años se han desarrollado dos alternativas con este objetivo. La genómica de células individuales permite secuenciar genomas ambientales y la reconstrucción de genomas a través de metagenomas usa el contenido de ADN de la comunidad como material de partida. En esta tesis, he estudiado genomas usando estas dos estrategias en muestras de agua de zonas relativamente poco exploradas como el Océano Índico Norte y el Océano Ártico. El Océano Índico Norte está sujeto a afloramientos estacionales de agua profunda rica en nutrientes que favorecen el crecimiento masivo de fitoplancton en superfície. La producción primaria es tal que el metabolismo heterotrófico que se nutre de productos derivados de fitoplancton consume la mayoría la oxigeno disponible, generando zonas mínimas de oxigeno (OMZ). Éstas se mantienen por procesos físicos que impiden su mezcla con otras masas de agua. Se prevé que estas zonas aumentarán debido al calentamiento global. Además han captado el interés de los ecólogos microbianos porque son aguas ricas en microorganismos involucrados en el ciclo del nitrógeno, y en metabolismos micro-aerobios y anaeróbicos. A pesar de que en el Índico Norte exista una de las OMZ más extensas del planeta, su diversidad microbiana ha sido poco estudiada. Mediante genómica de células individuales obtuve 98 genomas ambientales del género Kordia de los cuales, tras su análisis de microdiversidad, se seleccionaron diez para su secuenciación y co-ensamblado. El genoma co-ensamblado fue revisado manualmente para generar un genoma de referencia casi completo. Describí la novedad taxonómica de la especie con filogenias y análisis de genómica comparada con otras especies del mismo género. También definí su potencial metabólico y nicho de preferencia combinando la anotación funcional con su distribución en distintos metagenomas de la columna de agua de origen, de distintas profundidades y tamaños de plancton. El Océano Árctico tiene un gran impacto en la regulación climática de nuestro planeta, siendo actualmente severamente afectado por el calentamiento global. La diversidad procariótica de sus aguas se ha estudiado en muestreos esporádicos, mayormente centrados en estaciones del año específicas o en ciertas regiones geográficas. En esta tesis he construido 3550 genomas a partir de metagenomes Árticos, de diferentes regiones y durante distintas estaciones del año, los cuales representan casi la mitad del contenido genético de la comunidad. De estos, 530 se pueden clasificar como genomas de calidad media y alta, e incluyen una mayoría de taxones no descritos hasta ahora, cuya novedad taxonómica es incluso a nivel de Clase en el caso de las Bacterias. He estudiado sus implicaciones en el ciclo del carbono en el Ártico, sus patrones de distribución y sus preferencias de hábitat, definiendo generalistas y especialistas que pueden servir como especies centinela en futuros estudios de cambio climático en el Ártico. En resumen, esta tesis aporta una nueva visión en la diversidad funcional y taxonómica de procariotas marinos no cultivados, y propone nuevas metodologías para mejorar el ensamblaje de genomas y controles de calidad en los mapeos meta-ómicos. Durant les últimes dècades s'han aplicat noves tècniques d'estudi dels microorganismes marins per investigar aquells que no creixen en cultiu. La combinació de metodologies independents de cultiu, seqüenciació massiva i mostrejos oceanogràfics a gran escala ens han permès explorar una diversitat taxonòmica i funcional de microorganismes marins fins ara desconeguda. Els microorganismes marins juguen un paper fonamental en els cicles dels nutrients i la regulació del clima. Per això, és vital que definim la seva taxonomia, distribució, hàbitats i propietats funcionals a l'oceà. Relacionar taxonomia i funció sempre ha estat un repte en aquesta disciplina, però en els últims anys s'han desenvolupat dues alternatives que persegueixen aquest objectiu. La genòmica de cèl·lules individuals permet seqüenciar genomes ambientals i la reconstrucció de genomes a partir de metagenomes aprofita el contingut total d'ADN de la comunitat. En aquesta tesi, he generat genomes mitjançant aquestes dues estratègies en mostres d'aigua de zones relativament menys explorades com l'Índic Nord i l'Oceà Àrtic. L'Índic Nord és subjecte d'afloraments estacionals d'aigua profunda rica en nutrients, que a superfície afavoreixen el creixement de fitoplàncton. La producció primària a la superfície és tal que el metabolisme heterotròfic que es nodreix dels productes derivats del fitoplàncton consumeix la majoria d'oxigen, generant zones mínimes d'oxigen (OMZ) que es mantenen gràcies a processos físics que eviten que es mesclin amb altres masses d'aigües. Aquestes OMZ s'ha predit que augmentaran per l'escalfament global i han atret l'atenció d'ecòlegs microbians perquè són riques en microorganismes relacionats amb el cicle del nitrogen i diversos metabolismes micro-aerobis i anaerobis. Tot i que l'Índic Nord presenti una de les OMZ més extenses, la diversitat microbiana d'aquest ambient s'ha estudiat poc. Mitjançant genòmica de cèl·lules individuals vaig obtenir 98 genomes ambientals del gènere Kordia, dels que se'n van seqüenciar deu, després d'analitzar-ne microdiversitat. El seu co-assemblatge es va revisar manualment per generar un genoma de referència gairebé complet. Vaig descriure la nova espècie amb múltiples filogènies i anàlisis de genòmica comparada amb altres espècies del mateix gènere. També vaig definir el seu potencial metabòlic i nínxol de preferència combinant la seva anotació funcional amb la distribució a varis metagenomes de la columna d'aigua d'origen, incloent-hi diferents fondàries i mides de plàncton. L'Oceà Àrtic té un gran impacte a la regulació climàtica del nostre planeta i està severament afectat per l'escalfament global. La diversitat procariòtica de les seves aigües s'ha estudiat en mostrejos esporàdics, majoritàriament centrats en estacions de l'any concretes o certes regions geogràfiques. En aquesta tesi he construït 3550 genomes a partir de metagenomes de diferents regions àrtiques i durant diverses estacions de l'any, en una circumnavegació de les aigües l'Oceà Àrtic. Representen gairebé la meitat del contingut genètic de les comunitats i d'aquests, 530 es poden classificar com a genomes de qualitat mitjana i alta. Inclouen una elevada novetat taxonòmica, sobretot a nivell d'espècie però fins i tot a nivell de Classe, pel que fa als Bacteris. He estudiat les seves implicacions al cicle del carboni a l'Àrtic, així com la seva distribució i preferències d'hàbitat, definint generalistes i especialistes que poden servir com a espès sentinella en futurs estudis de canvi climàtic a l'Àrtic. En resum, aquesta tesi aporta una nova visió en la diversitat funcional i taxonòmica de procariotes no cultivats i proposa noves metodologies per millorar l'assemblatge de genomes i controls de qualitat en els mapejos meta-òmics.

Les diatomées (Stramenopiles, Bacillariophyceae) jouent un rôle important sur le plan écologique et sont l'un des groupes phytoplanctoniques les plus divers, avec environ 1800 espèces planctoniques estimées. Bien que largement étudiées, leurs modèles de diversité et de distribution biogéographique ne sont pas bien connus. L'avènement du séquençage de l'ADN à haut débit a révolutionné les études de biodiversité moléculaire facilitant la compréhension de la biogéographie, de la structure des communautés et des processus écologiques. Les deux principaux objectifs de cette thèse sont (1) d'enquêter sur les modèles de la biodiversité mondiale et la structure des communautés de diatomées planctoniques à travers les océans du monde, et (2) de comprendre les mécanismes et processus déterminants la structure de la communauté. Cette thèse présente également une première tentative de discerner la répartition des espèces rares dans les communautés de protistes. L'étude a été réalisée en utilisant les données de metabarcoding générées à partir des échantillons biologiques et des données environnementales associées recueillies au cours de la campagne Tara Oceans (2009-2013), une circumnavigation globale couvrant toutes les principales provinces océaniques. Le matériel d’étude pour cette thèse est constitué d’un total de 12 millions de séquences de la sous unité V9 du 18S ribosomal (barcode), récoltées à partir de 46 stations soit 293 échantillons. Basée sur 63371 metabarcodes de diatomées uniques, cette étude présente une évaluation approfondie de la distribution mondiale des diatomées et de leur diversité. Les analyses révèlent des faits marquants liées à la biogéographie des diatomées, par exemple une nouvelle estimation du nombre total d'espèces de diatomées planctoniques, une diversité considérable inconnue, une diversité exceptionnellement élevée en haute mer, et des patrons de diversité complexes entre les provinces océaniques. La thèse examine ensuite les facteurs qui déterminent les modèles de bêta-diversité. Les résultats suggèrent que les diatomées sont des communautés structurées et réglementées par l'hétérogénéité de l'environnement et des processus spatiaux. Néanmoins, la majorité de la variation totale dans la composition de la communauté ne peut être expliquée ni par les facteurs environnementaux, ni par les distances spatiales, ce qui justifie les analyses futures se concentrant sur les interactions biologiques, les événements historiques, et d'autres facteurs qui ne sont pas considérés. La thèse décrit en outre une approche pour caractériser les clusters significativement associés de ribotypes concomitants. Enfin, une étude préliminaire de communautés de protistes fractionnées par taille révèle que la queue (de leurs distributions rang abondance) semble suivre un comportement en loi de puissance dans presque toutes les communautés de protistes. Cette observation peut indiquer un mécanisme universel potentiel qui peut expliquer l'organisation de communautés planctoniques marines. De façon générale, ce travail présent une perspective globale et complète de la distribution et de la diversité des diatomées dans les océans du monde. La thèse propose un cadre global pour l'évaluation de la diversité mondiale basée sur le metabarcoding, qui pourra être utilisé pour étudier la distribution et la diversité des autres lignées taxonomiques. Par conséquent, ce travail fournit un point de référence pour explorer comment les communautés microbiennes feront face à la variation des conditions environnementales. Diatoms (Stramenopiles, Bacillariophyceae) are an ecologically important and one of the most diverse phytoplanktonic groups, with an estimated ~1,800 marine planktonic species. Although widely studied, their diversity and biogeographic distribution patterns are not well known. The advent of high-throughput DNA sequencing has revolutionized molecular biodiversity studies facilitating the understanding of biogeography, community assembly and ecological processes. The two major goals of this thesis are (1) to investigate global biodiversity patterns and structure of marine planktonic diatom communities across the world’s oceans, and (2) to understand the mechanisms and processes determining their community structure and assembly. This thesis also presents an initial attempt to discern the distribution of rare species in protist communities. The study was conducted using the metabarcoding data generated from the biological samples and associated environmental data collected during the Tara Oceans (2009-2013) global circumnavigation covering all major oceanic provinces. A total of ~12 million diatom V9-18S rDNA tags from 46 sampling stations, constituting 293 size fractionated samples represent the study material for the thesis. Using 63,371 unique diatom metabarcodes, this study presents an in-depth evaluation of global diatom distribution and diversity. The analyses study draw a number of revelations related to diatom biogeography, e.g. a new estimate of the total number of planktonic diatom species, a considerable unknown diversity, exceptionally high diversity in the open ocean, complex diversity patterns across oceanic provinces. The thesis then looks into the factors determining the beta-diversity patterns. The results suggest that diatoms represent biogeographically structured ecological communities regulated by both environmental heterogeneity and spatial processes. Nonetheless, the majority of the total variation in community composition remained unexplained by either the examined measured environmental factors or spatial distances, which warrants future analyses focusing on biological interactions, historical events, and other factors that are not considered. The thesis further outlines an approach to characterize significantly associated clusters of co-occurring ribotypes. Finally, a preliminary study of size-fractionated protistan communities reveals that the tail (of their rank-abundance distributions) appears to follow a power-law behavior in almost all protistan communities. This observation may indicate a potential universal mechanism which can explain the organization of marine planktonic communities. In general, this work has presented a global comprehensive perspective on diatom distribution and diversity in the world’s oceans. The thesis offers an overall framework for metabarcoding-based global diversity assessments which in turn can be employed to study distribution and diversity of other taxonomic lineages. Consequently, this work provides a reference point to explore how microbial communities will respond/change in response to environmental conditions.