La lignée verte (i.e. les plantes) est représentée dans l'océan par les algues appartenant aux Chlorophyta. Celles-ci contribuent en moyenne à 25% des séquences photosynthétiques (Dinoflagellés exclus) retrouvées dans les inventaires moléculaires pan-océanique. Bien que les Chlorophyta jouent un rôle important dans l'écologie de l'océan et nous permettent de comprendre l'histoire évolutive des plantes terrestres, leur diversité et leur distribution dans les eaux marines du globe est peu documentée. Après avoir optimisé une base de données de séquences de références ARNr 18S, j'ai procédé à l'analyse de données de métabarcodes produits par Ocean Sampling Day (OSD), qui a fourni des données utilisant 2 régions hypervariables du gène du 18S appelées V4 et le V9. La comparaison des images de diversité produites par le V4 et le V9 a illustré l'influence de la base de référence sur la diversité. Ensuite, l'analyse de l'ensemble des V4 a permis d'étudier la distribution des Chlorophyta dans l'océan mondial. De plus, la vérification de l'assignation automatique des OTUs par reconstruction phylogénétique grâce à la base de référence produite en début de thèse, a permis de confirmer l'existence de nouvelles lignées de prasinophytes et de confirmer que la classe des Mamiellophyceae dominait les eaux côtières, alors que les clades VII et IX des prasinophytes dominaient les eaux océaniques oligotrophiques. Ces analyses ont aussi permis de montrer l'écart entre la diversité environnementale et celle dans la base de référence, en particulier pour les genres Ostreococcus et Micromonas (Mamiellophyceae). / The green lineage that dominates on land is represented by Chlorophyta which account in average for 25% of photosynthetic sequences (Dinoflagellates excluded) in global marine molecular inventories. Although Chlorophyta are major keys for ecological understanding of the ocean, as well as the evolutionary story understanding of land plants, their diversity and distribution in marine waters has been understudied. This thesis aims at investigating the environmental diversity of marine Chlorophyta and describing their distributions based on available large scale metabarcoding datasets. First, a reference database of publicly available 18S rRNA sequences of Chlorophyta was assembled and critically curated. Next, the Ocean Sampling Day (OSD) 18S metabarcode datasets were analysed. Chlorophyta diversity was compared for a limited sample set based on two regions of the 18S rRNA: the V4 and V9 regions. Then, Chlorophyta distribution was studied using the full OSD V4 dataset. Careful taxonomic investigations using both automatic and hand checked assignation of OTUs using alignments and phylogenies allowed to confirm the existence of new environmental prasinophytes clades and to confirme, that the Mamiellophyceae were the major group in coastal waters, while prasinophytes Clade VII and IX were dominating the oceanic oligotrophic stations. Comparing V4 and V9 regions illustrated the influence of the reference database on diversity. Moreover, the taxonomic investigation highlighted the diversity gaps between reference databases and environmental datasets. This work emphasizes the neglected importance of Chlorophyta in marine waters and provides some suggestions for future research.

Euglenophyceae represent a group of unicellular eukaryotic organisms that have gained during their evolution the ability to photosynthesize. They aquired plastids via secondary endosymbiosis with a green alga as the plastid donor. Phylogenetic studies searching for the origin of this organelle revealed the green alga Pyramimonas parkeae from Prasinophytes as the closest known relative to euglenid plastids. Pyramimonas parkeae and Euglena share several genes clusters with unique order of genes in their plastid genomes, which also point to the Pyramimonadales as the donor of the plastids. However, it is posible, that organisms more closely related to euglenid plastids than P. parkeae, occur in the environment. In my diploma thesis I focused on the exploration of diversity of Pyramimonadales and Euglenophyceae in environmental samples. I used several approaches to perform this task. I amplified parts of the plastid genomes in environmental samples by using specific PCR and determined their position in the phylogenetic tree. I also made large-scale phylogenetic analyses based on 16S rRNA and 18S rRNA sequences from representatives of the groups Euglenophyceae, Prasinophytes and environmental samples. The results revealed the presence of a large number of environmental sequences relative to the...

Marine microbes are an essential component of global biogeochemical cycles. In oligotrophic marine surface waters, the phytoplankton, phototrophic, single-celled (on occasion, colonial) organisms, is often dominated by the picoplankton (cells <2 micrometers in size), which constitute the base of the marine food chain. The picophytoplankton is composed of three main groups of organisms: two genera of cyanobacteria, Prochlorococcus and Synechococcus, and a third group, the picoeukaryotes. Even though numerically less abundant than cyanobacteria, picoeukaryotes can contribute significantly to biomass and primary production in this size fraction. Furthermore, picoeukaryotes are a diverse group but this diversity is still underexplored and their ecological roles and physiology is poorly understood. Here uncultured protists are investigated using 18S rRNA gene clone libraries, phylogenetic analyses, specific fluorescence in situ hybridization (FISH) probes and other methods in tropical and subtropical waters. Gene sequences comprising a unique eukaryotic lineage, biliphytes, were identified in most samples, whether from high (30 degrees Celsius) or low (5 degrees Celsius) temperature waters. Sequences within this uncultured group have previously been retrieved from mid and high latitudes. Phycobilin-like fluorescence associated with biliphyte-specific FISH probed cells indicated they may be photosynthetic. Furthermore, the data indicated biliphytes are nanoplanktonic in size, averaging between 3.0 and 4.1 micrometers. Using the 18S rRNA gene, sequences belonging to a broadly distributed but uncultivated pico-prymnesiophytes were retrieved. We investigated the ecological importance of these natural pico-prymnesiophyte populations and field experiments showed that they could grow rapidly and contributed measurably to primary production. They also appear to form a large portion of global picophytoplankton biomass, with differing contributions in five biogeographical provinces, from tropical to high latitudes. Finally, the physiology of the picoeukaryote Micromonas was studied under a shift from medium to high light and UV radiation. Results showed that the growth of these photosynthetic cells was synchronized with the light: dark period. Forward angle side scatter and red autofluorescence from chlorophyll increased throughout the light period and decreased during the dark period. This is consistent with cell division occurring at the beginning of the dark period. Additionally, genes proposed to have roles in photoprotection were up-regulated under high light and UV, but not in controls.

One of the most important events in the history of life is the evolution of the complex, eukaryotic cell. The eukaryotes are complex organisms with membrane-bound intracellular structures, and they include a variety of both single-celled and multicellular organisms: plants, animals, fungi and various protists. The evolutionary origin of this group may be studied by direct evidence of past life: fossils. The oldest traces of eukaryotes have appeared by 2.4 billion years ago (Ga), and have additionally diversified in the period around 1.8 Ga. The Mesoproterozoic Era (1.6-1 Ga) is characterised by the first evidence of the appearance complex unicellular microfossils, as well as innovative morphologies, and the evolution of sexual reproduction and multicellularity. For a better understanding of the early eukaryotic evolution and diversification patterns, a part of this thesis has focused on the microfossil records from various time periods and geographic locations. Examination of microfossil morphology, cell wall microstructure and biochemical properties, reflect their intracellular complexity and function, and allow reconstructions of their life cycle, as well as observing the evolutionary pattern of change from Mesoproterozoic, to Cambrian-Ordovician transition. Several case studies included assemblages deriving from Mesoproterozoic, Neoproterozoic and early Paleozoic time intervals that show disparate morphotypes and innovative features indicative of algal clades. The Mesoproterozoic Ruyang Group in northern China has yielded a diverse microfossil assemblage that provides important clues about the diversification of different eukaryotic groups. Furthermore these microfossils contributed an additional evidence for the emergence of the crown group Eukarya by 1.7-1.4 Ga. In another part of this thesis, examination of wall microstructure and chemical properties via Raman spectroscopy has been used to assess the biological affinities of various Neoproterozoic problematic carbonaceous compression fossils. Studies on the early Phanerozoic (c. 545-485 Ma) assemblages from Estonia reconstructed patterns of the early radiations of phytoplankton and its evolutionary innovations. A continuing theme in this thesis has been using a combination of evidence of microfossils’ fine-scale morphology, ecology and chemical properties to determine their function in life, in addition to their systematic position. / Palaeobiology and diversification of Proterozoic-Cambrian photosynthetic eukaryotes

The present study focuses on the Emsian-Eifelian (Lower-Middle Devonian) carbonate sequences of the Prague Basin. The Třebotov Limestone (Daleje-Třebotov Formation) and the Choteč Limestone (Choteč Formation) and their equivalents represent the stratigraphic units studied. The main goal of this study is to characterize environmental changes, known as Basal Choteč event, that were described from the boundary interval of the Třebotov and Choteč Limestone. In order to do so, sedimentological (microfacies analysis), geochemical (δ13 Ccarb, δ18 Oapatite) and paleontological (taxonomy of conodonts) studies were carried out. Eight microfacies types of carbonate rocks were described and interpreted in this study. Beside that, massive accumulations of calcispheres, peloids, prasinophytes and occurrences of blue-green algae (Girvanella) were recorded especially in the Choteč Limestone. The multidisciplinary approach mentioned resulted in characterization of the sedimentary environment of the studied units as well as their development in time. The main result of the present study is the model of the Basal Choteč event. A hypothesis of enhanced nutrient load is suggested here as a triggering mechanism for intense micritization and peloid formation and prasinophyte blooms, which were together with greater...