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The Tara Oceans project sampled contrasting ecosystems of the world oceans during a three-year expedition (2009-2013), collecting environmental data and plankton, from viruses to metazoans, on board the 36-metre Tara Schooner. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. Samples were later analysed using modern sequencing and state-of-the-art imaging technologies., We are keen to thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON, BIOMARKS, PROMETHEUS, and TARA-GIRUS), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without the continuous support of the participating 23 institutes

International audience; Collodaria are ubiquitous and abundant marine radiolarian (Rhizaria) protists. They occur as either large colonies or solitary specimens, and, unlike most radiolarians, some taxa lack silicified structures. Collodarians are known to play an important role in oceanic food webs as both active predators and hosts of symbiotic microalgae, yet very little is known about their diversity and evolution. Taxonomic delineation of collodarians is challenging and only a few species have been genetically characterized. Here we investigated collodarian diversity using phylogenetic analyses of both nuclear small (18S) and large (28S) subunits of the ribosomal DNA, including 124 new sequences from 75 collodarians sampled worldwide. The resulting molecular phylogeny was compared to morphology-based classification. Our analyses distinguished the monophyletic clade of skeleton-less and spicule-bearing Sphaerozoidae from the sister clades Collosphaeridae (skeleton-bearing) and Collophidiidae (skeleton-less), while the Thalassicollidae was not retrieved as a monophyletic clade. Detailed morphological examination with electron microscopy combined with molecular analyses revealed many discrepancies, such as a mix between solitary and colonial species, co-existence of skeleton-less and skeleton-bearing specimens within the Collosphaeridae, as well as complex intraspecific variability in silicified structures. Such observations challenge a morphology-based classification and highlight the pertinence of an integrative taxonomic approach to study collodarian diversity. (C) 2015 Elsevier GmbH. All rights reserved.

Collodaria (Radiolaria) are unicellular marine eukaryotes (protists) belonging to the super-group Rhizaria. Collodarian species contribute to planktonic communities as large solitary cells or can form large gelatinous colonies. They are heterotrophic organisms feeding on other plankton, which also systematically harbour intracellular symbiotic microalgae. Recent environmental molecular diversity surveys demonstrated their important contribution to planktonic communities and their worldwide occurrence in the global ocean. However, knowledge on their diversity, biogeography and ecology is paradoxically very poor. In the first part of this thesis I performed detailed morphological analyses (electron and optical microscopy) combined with a molecular phylogeny based on the 18S and 28S rRNA genes, sequencing for a total of 75 distinct colonial and solitary specimens. Ultimately, this work led to the revision of the Collodaria classification and to the construction of a robust morpho-molecular reference database. Then, this morpho-molecular framework allowed the exploration of Collodaria biodiversity through a metabarcoding approach across samples collected in the global ocean during the Tara Ocean expedition. The cosmopolitan distribution of the different collodarian taxa in the surface oceans revealed a higher biodiversity in the vast oligotrophic inter-tropical open oceans. Collosphaeridae were predominantly found in the open oceans while the Sphaerozoidae were the dominant family in the less diverse coastal regions. The newly defined Collophidiidae were rarely encountered in the photic zones at all latitudes, suggesting that they inhabit a different ecological niche. Finally, I also used the in situ imaging system Underwater Vision Profiler (UVP5) to quantitatively explore the abundances and biomasses of collodarian and rhizarian in the global ocean. This approach revealed that the Rhizaria were a major component of the meso- and macro-plankton, constituting up to 4.5% of the global carbon standing stock in the upper 200 m of the world oceans. More specifically, Collodaria were the most important rhizarian groups in the first 100 m of the oceans, and their distribution suggested that photosymbiosis might be an important factor explaining their success in oligotrophic regions where they are particularly abundant. Besides the improvement of our knowledge on the diversity, biogeography and ecology of Collodaria in the global ocean, this thesis highlights the relevance to combine and/or use alternative sampling and analytical procedures such as high-throughput sequencing and in situ imaging technologies to study marine protists in their environment., Les Collodaires (Radiolaires) sont des eucaryotes unicellulaires (protistes) marins appartenant au super-groupe des Rhizaria. Tandis que certains sont caractérisés par un mode de vie colonial, d’autres sont observés sous la forme de larges organismes solitaires. Les Collodaires sont des protistes hétérotrophes, prédateurs de plancton, mais également hôtes systématiques de micro-algues photosynthétiques intracellulaires. Les récentes analyses de leur diversité moléculaire dans l’environnement ont démontré leur importante contribution aux communautés planctoniques ainsi que leur distribution globale dans l’océan mondial. Cependant, nos connaissances sur leur diversité, biogéographie et écologie restent paradoxalement parcellaires. La première partie de cette thèse a été dédiée à des études morphologiques détaillées (en microscopie électronique et optique) et combinées à une phylogénie moléculaire élaborée en séquençant les sous-unités 18S et 28S de l’ADN ribosomal pour 75 spécimens, coloniaux ou solitaires. Ce travail a abouti à la réévaluation de la classification des Collodaires et à l’élaboration d’une base de référence morpho-moléculaire robuste. Par la suite, ce cadre de référence morpho-moléculaire a permis d’explorer la biodiversité des Collodaires grâce à une approche de metabarcoding appliquée à une série d’échantillons collectés dans l’océan mondial pendant l’Expédition Tara Océans. La distribution cosmopolite à la surface des océans des différents taxons qui composent les Collodaires, a révélé une diversité plus importante dans les vastes régions océaniques intertropicales et oligotrophiques. Les Collosphaeridae ont été principalement observés en pleine mer alors que les Sphaerozoidae formaient la famille dominante dans les régions côtières, où la biodiversité des Collodaires était plus faible. Les Collophidiidae, formellement décrits au cours de thèse, ont rarement été rencontrés dans les zones photiques, quelque que soit la latitude, suggérant ainsi qu’ils occupent une niche écologique particulière. Enfin, j’ai également employé la technologie d’imagerie in situ Underwater Vision Profiler (UVP5) afin d’explorer de façon quantitative les abondances et biomasses des Collodaires et des Rhizaria, à travers l’océan mondial. Cette approche a révélé que les Rhizaria forment un composant majeur du méso- et macro-plancton, et représentent jusqu’à 4,5% de la biomasse globale des 200 premiers mètres de l’océan mondial. Plus particulièrement dans les 100 premiers mètres, les Collodaires constituent le groupe le plus important des Rhizaria et leur distribution suggère que la photosymbiose pourrait influencer leur succès dans les régions oligotrophiques où ils sont particulièrement abondants. Au-delà d’améliorer notre compréhension de la diversité, la biogéographie et l’écologie des Collodaires dans l’océan mondial, ce travail de thèse souligne la pertinence de combiner et d’utiliser des approches alternatives d’échantillonnage et d’analyses tel que le séquençage haut-débit et l’imagerie in situ dans l’étude des protistes marins dans leur environnement.

Radiolaria are unicellular holoplanktonic protozoa with siliceous or strontium sulfate skeletons. Mainly studied by micropaleontologists because of their excellent fossil record, they are also key members of planktonic communities and play important roles in various oceanic ecosystems. This chapter presents an overview of the current knowledge on living Radiolaria (orders Acantharia, Collodaria, Nassellaria, Spumellaria and Taxopodia). Besides general considerations on Radiolaria as a whole, it focuses on the taxonomy, biology, and ecology of each radiolarian order. Finally this chapter provides insights on research perspectives to improve our knowledge of living radiolarians and their ecological role in marine ecosystems.