Visual assessment of discontinuities in the morphological features of diatom cells has been widely used in the discovery and delimitation of diatom species. However, a multidisciplinary approach to species-level taxonomy has revealed hidden diversity within the traditional diatom morphospecies. Consequently, this work examined both the natural and clonal populations of diatoms by diverse traditional and modern approaches, in order to assess the diversity, ecology, and distribution of diatom species. Although a detailed investigation of natural diatom samples was confounded by uncertain morphological boundaries between the traditional diatom species, it recognized that the diversity was relatively high; even one new diatom species was described using the morphological species concept. The multivariate statistical analyses showed that the variation of natural communities of traditional diatom morphospecies reflected differences in the local environmental conditions, as well as microhabitat heterogenity within a region. Since each diatom morphospecies is most likely a complex of sibling species, the two model traditional morphospecies were investigated, in order to assess morphological variation, genetic diversity, and/or the reproductive compatibility of monoclonal cultures. Even though isolated...

Les espèces protistes ont été traditionnellement classifiées comme des plantes ou des animaux en raison de l’absence ou présence des chloroplastes. L’état actuel de la connaissance indique qu’un grand nombre d’espèces protistes portent des chloroplastes mais que physiologiquement elles sont capables d’utiliser l’autotrophie (photosynthèse) ou l’hétérotrophie pour se nourrir. La combinaison de ces deux modes trophiques par une même cellule est nommée mixotrophie. Chez les protistes l’hétérotrophie peut s’effectuer soit par la consommation des particules par phagocytose, e.g. des proies bactériennes, ou bien par l’absorption des composants organiques dissouts, i.e. osmotrophie. La mixotrophie est de plus en plus décrit chez les protistes dans tous les habitats aquatiques. Les écologistes du plancton constatent la récurrence de la mixotrophie chez les formes traditionnelles « phyto»plancton et micro »zoo »plancton. Cependant, identifier et quantifier la mixotrophie reste toujours un défi méthodologique. Dans cette étude nous nous sommes intéressés à la mixotrophie chez les espèces phytoplanctoniques marines, en particulier à leur nutrition phagotrophique de proies bactériennes. Nous avons testé des techniques modernes afin d’identifier la mixotrophie dans des cellules phytoplanctoniques. La technique cytogénétique d’hybridation in situ Card-FISH en utilisant de sondes d’ARN ribosomique 16S a été effectuée suivant des protocoles existant pour des bactéries et des protistes. Cette technique s’est avérée être un outil précieux pour visualiser des groupes phylogénétiques bactériens en association avec le phytoplancton à l’aide de la microscopie à épifluorescence, sans avoir besoin d'un isolement préalable des cellules ou des interférences avec l'association microbienne. Cependant, la méthode a échoué pour visualiser mixotrophie chez le phytoplancton car la sonde eubactérienne générale(EUB338) combine une large gamme d'espèces phytoplanctoniques, ce qui rend impossible de discriminer les signaux fluorescents provenant de tissus bactérienne ou phytoplanctonique. Le contexte de ces études est le phytoplancton et les bactéries hétérotrophes lesquels constituent des principaux concurrents pour les nutriments inorganiques dissouts. Dans le cas où la croissance bactérienne est limitée par le carbone, l'augmentation de la concentration de carbone organique dissous(DOC) renforce la croissance bactérienne et la consommation de nutriments dissous et ainsi affecte négativement la croissance du phytoplancton autotrophe. Cependant, les consommateurs de bactéries, i.e.phytoflagellés mixotrophes, peuvent être favorisés dans de telles situations car la hausse de DOC donne lieu à l'abondance plus élevé des proies bactériennes.En outre, nos résultats indiquent un potentiel effet positif de la température sur le mode de nutrition hétérotrophe de l’espèce, ainsi qu’une croissante contribution des espèces mixotrophes au sein des communautés de phytoplancton dans des conditions des hautes températures des eaux de surface de la mer. / Protist species were traditionally classified morphologically as either „plants“ or „animals“, based on the absence or presence of chloroplasts. State of science is that a high number of protist species carrychloroplasts but are nutritionally able to employ both autotrophy (photosynthesis) and heterotrophywithin a single cell. This combination of autotrophic and heterotrophic mode of nutrition within a single species is named mixotrophy. In protists, heterotrophy can be realized either by the uptake of food particles (e.g. bacterial prey) through phagocytosis or by the uptake of dissolved organic compounds (i.e.osmotrophy). Mixotrophy is globally and increasingly described in protists from all types of aquatic habitats. Plankton ecologists nowadays assess mixotrophy among the traditionally typified “phyto”plankton and mikro”zoo”plankton species as regularity. Nevertheless, detection and quantification of mixotrophy is still a methodological challenge. In this study, we focused on mixotrophy in marine phytoplankton species and put emphasis on its phagotrophic nutrition from heterotrophic bacterial prey. State of the art methodology was tested to visualize mixotrophy in single phytoplankton cells. Catalyzedreported deposition-fluorescence in situ hybridization (Card-FISH), using 16S ribosomal RNA probes,was employed based on existing protocols for bacteria and protists. The method proved to be a valuable tool to visualise bacterial phylogenetic groups in association with phytoplankton by epifluorescence microscopy without need for prior isolation of cells or interference with the microbial association.However, the method failed to visualize mixotrophy in phytoplankton since the general eubacterial probe(EUB338) hybridised a broad range of phytoplankton species making it impossible to discriminate fluorescent signals originating from bacterial or phytoplankton tissue. Background of these studies is phytoplankton and heterotrophic bacteria being major competitors for dissolved inorganic nutrients. In case that bacterial growth is carbon limited, increasing concentrations of degradable dissolved organic carbon (DOC) enhance bacterial growth and consumption of dissolved nutrients and there by negatively affect autotrophic phytoplankton growth. Bacteria consuming mixotrophic phytoflagellates, however, may gain in importance in such situations since DOC provokes higher bacterial prey supply.In addition, our results indicate a potential positive effect of temperature on O. minima´s heterotrophic nutrition mode, and indicate a potential increasing contribution of mixotrophic species to phytoplankton communities under increasing sea surface water temperatures.

Endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex tethering ER and mitochondria. ERMES consists of four core subunits - Mmm1, Mmm2 (Mdm34), Mdm10 and Mdm12. It was first discovered in Saccharomyces cerevisiae and most functional information is based on studies of this organism. ERMES affects mitochondrial distribution and morphology, participates in lipid trafficking and is important for homeostasis of the cell. In Trichomonas vaginalis, the human urogenital parasite, three genes for putative, highly divergent components of ERMES complex were predicted. However, the cell localization of these proteins and their function is unknown. This thesis is focused on investigation of ERMES components in T. vaginalis, their cellular localization, interactions between components and identification of their possible interacting partners.

Dictyostelids (Amoebozoa) are a group of social amoebae consisting of approximately 150 species, which are found in terrestrial habitats worldwide. They are divided into eight major clades based on molecular phylogeny, and within these clades are many species complexes. Some species are seemingly cosmopolitan in distribution, while others are geographically restricted. In this thesis dictyostelids were recovered from high latitude habitats (soils in Sweden and Iceland) as well as from the soles of shoes. Morphological characters and DNA sequence analyses were used to identify isolates that were recovered and delimit new species, as well as to investigate the monophyly of Dictyostelium aureostipes. Nine species were reported from Northern Sweden and four from Iceland. Among the isolates recorded in Sweden were two new species, described as D. barbibulus and Polysphondylium fuscans. P. fuscans was among the four species recovered from footwear, contributing evidence for anthropogenic transport of dictyostelids. Ecological patterns were assessed using linear regression and generalized linear models. The ecological analyses of dictyostelids recovered from Iceland indicate that these organisms are most frequently found in soils of near-neutral pH, but also exhibit a species richness peak in moderately acidic soils. These analyses indicate that in Iceland dictyostelid species richness decreases with altitude, and in the northern hemisphere the species richness increases with decreasing latitude. A three-region analysis of the D. aureostipes species complex indicated that this species is in fact made up of at least five phylogenetically distinct clades, and in light of this the group is in need of taxonomic revision. These results indicate that the dictyostelid species richness is higher than previously known, especially in high-latitude regions, and that even seemingly well-defined species may harbour cryptic diversity. Presently, species ranges may be expanding via anthropogenic dispersal but despite this, the dictyostelids are found to exhibit biogeographic trends well known from macroorganisms, such as a latitudinal gradient of species richness.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Brown howler monkeys (Alouatta guariba clamitans) occur in the Brazilian Atlantic Forest from the states of Minas Gerais and Rio de Janeiro to Rio Grande do Sul, and in a small area in northestern Argentina. They are classified as Vulnerable in the state of Rio Grande do Sul due especially to the loss and fragmentation of their natural habitats, and also due to the deaths caused by the recent outbreak of sylvatic yellow fever (2008/2009). The intense human activities on natural habitats, besides the habitat loss, can favor the spread of pathogenic agents such as bacteria and other parasites which affect men and domestic animals, and which can also occur in wildlife animals. This study aimed at verifying the occurrence of Enterobacteriaceae and Cryptosporidium sp. in feces of free-ranging brown howler monkeys in Santa Maria, Rio Grande do Sul, Brazil, and understanding the influence of ecological and environmental factors (group size, howler population density, fragment size, distance to the nearest human settlement, distance to the nearest river and seasonality) on the richness of such organisms. The samples were analyzed at the Center for Studies and Research on Wild Animals (NEPAS / LCDPA) of the Federal University of Santa Maria. Twenty Enterobacteriaceae species were detected, and with the techniques employed, the samples were negative for Salmonella spp. and Cryptosporidium sp. None of the environmental variables had significant influence on the wealth of Enterobacteriaceae. Considering that howler populations at CISM (Campo de Instrução de Santa Maria) fell dramatically due to yellow fever, and that some organisms found in this study may interact with other factors and affect the population dynamics of the howler. We believe that it is fundamental to continue monitoring the health of these populations in order to better understand disease mechanisms, as well as conserve this species. / O bugio-ruivo (Alouatta guariba clamitans) ocorre na Mata Atlântica dos estados de Minas Gerais e Rio de Janeiro ao Rio Grande do Sul e em pequena porção do nordeste da Argentina. É classificado como vulnerável no Rio Grande do Sul devido principalmente à perda e fragmentação de habitat e ao recente surto de febre amarela silvestre (2008/2009). As intensas atividades antrópicas no meio selvagem, além da perda de habitat, podem favorecer a disseminação de agentes patogênicos como bactérias e parasitos, que ocorrem em animais domésticos e em humanos e que podem acometer também os animais selvagens. O objetivo deste estudo foi verificar a ocorrência de bactérias da família Enterobacteriaceae e do protista Cryptosporidium sp. em fezes de bugios-ruivos de vida livre no município de Santa Maria, Rio Grande do Sul, Brasil, bem como relacionar a riqueza de enterobactérias nas amostras com fatores ecológicos e ambientais como tamanho do grupo, tamanho do fragmento florestal, densidade de populações de bugios, distância com núcleos humanos mais próximos, distância para cursos d água e sazonalidade. As amostras foram analisadas no Núcleo de Estudos e Pesquisas em Animais Silvestres (NEPAS/LCDPA) da Universidade Federal de Santa Maria. Foram detectadas vinte espécies de enterobactérias, e com as técnicas empregadas, as amostras foram negativas para Salmonella spp. e Cryptosporidium sp.. Nenhuma das variáveis ambientais analisadas teve influência sobre a riqueza das enterobactérias. Considerando que as populações de bugios do Campo de Instrução de Santa Maria (CISM) sofreram uma drástica redução devida à febre amarela, e que alguns organismos encontrados nesse estudo podem estar interagindo com outros fatores e assim afetar a dinâmica populacional dos bugios. Acredita-se que a continuidade do monitoramento da saúde destas populações seja fundamental para melhorar a compreensão dos mecanismos das doenças, assim como para a conservação dessa espécie.

Following their endosymbiotic uptake, plastids undergo profound changes to genome content and to their associated biochemistry. I have investigated how evolutionary transitions in plastid genomes may impact on biochemical pathways associated with plastid gene expression, focusing on the highly unusual plastids found in one group of eukaryotes, the alveolates. The principal photosynthetic alveolate lineage is the dinoflagellate algae. Most dinoflagellate species harbour unusual plastids derived from red algae. The genome of this plastid has been fragmented into small, plasmid-like elements termed “minicircles”. Transcripts of this genome receive a 3’ poly(U) tail and, in some species, undergo extensive sequence editing. Some dinoflagellates have replaced their original plastids with others, in a process termed “serial endosymbiosis”. The major non-photosynthetic alveolates are the apicomplexans, which include the malaria parasite Plasmodium. Apicomplexans are descended from free-living algae and possess a vestigial plastid, which originated through the same endosymbiosis as the ancestral red dinoflagellate plastid. This plastid has lost all genes involved in photosynthesis and does not possess a poly(U) tail addition pathway. I have investigated the consequences of the fragmentation of the red algal dinoflagellate plastid genome on plastid transcription. I have characterised non-coding transcripts in plastids of the dinoflagellate Amphidinium carterae, including the first evidence for antisense transcripts in an algal plastid. Antisense transcripts in dinoflagellate plastids do not receive poly(U) tails, suggesting that poly(U) tail addition may play a role in strand discrimination during transcript processing. I have additionally characterised transcript processing in dinoflagellate plastids that were acquired through serial endosymbiosis. I have shown that poly(U) tail addition and editing occur in the haptophyte-derived serial endosymbionts of the fucoxanthin-containing dinoflagellates Karenia mikimotoi and Karlodinium veneficum. This is the first evidence that plastids acquired through serial endosymbiosis may be supported by pathways retained from previous symbioses. Transcript editing constrains the phenotypic consequences of divergent mutations in fucoxanthin plastid genomes, whereas poly(U) tail addition plays a central role in recognising and processing translationally functional fucoxanthin plastid mRNAs. I have additionally shown that certain genes within fucoxanthin plastids are located on minicircles. This demonstrates convergent evolution in the organisation of the fucoxanthin and red algal dinoflagellate plastid genomes since their endosymbiotic acquisition. Finally, I have investigated transcript processing in the algae Chromera velia and Vitrella brassicaformis. These species are closely related to apicomplexans but are still photosynthetic and apply poly(U) tails to plastid transcripts, as with dinoflagellates. I have shown that poly(U) tails in these species are preferentially associated with translationally functional mRNAs of photosynthesis genes. This is the first plastid transcript processing pathway documented to target a specific functional gene category. Poly(U) tail addition may direct transcript cleavage and allow photosynthesis gene transcripts to accumulate to high levels. The loss of this pathway from ancestors of apicomplexans may have contributed to their transition from photosynthesis to parasitism.

Charles University, Faculty of Science Department of parasitology Doctoral study programme: Parasitology Abstract (en) Analysis of the genome of a free-living amoeba Mastigamoeba balamuthi and its comparison with pathogenic Entamoeba histolytica Mgr. Vojtěch Žárský Supervisor: prof. RNDr. Jan Tachezy, Ph.D. Praha, 2020 Abstract Examination and comparison of organisms have been tremendously important for the study of life's history on earth. The progress of our understanding of the genetic basis of heredity and the recent boom of sequencing technologies allows us to continue in this exciting field of research from the perspective of genes and genomes. In this work, I focus on the study of an anaerobic amoeba Mastigamoeba balamuthi, which is related to an important human pathogen Entamoeba histolytica. Comparative analysis allows us to draw some conclusions about the nature of the common ancestor of Mastigamoeba and E. histolytica, how it adapted to the anaerobic lifestyle, and about the way the Entamoeba lineage evolved to become a successful parasite. Surprisingly we also noticed that besides hydrogenosomes (hydrogen-producing organelles related to mitochondria), M. balamuthi also harbors peroxisomes - organelles thought to be absent in anaerobic organisms. This finding motivated us to inquire more about...

The overall aim of this study was to investigate the potential influence of chitosan, a biodegradable and antimicrobial compound, on termite hindgut symbionts. For this purpose, a morphological quantifying technique was conducted on the protist community’s hindgut after feeding termites on chitosan-treated wood. The aim was to characterize the diversity of protist species in the economically important dark southern subterranean termite, Reticulitermes virginicus. A molecular phylogenetic analysis of the V3 and V4 hyper-variable regions of 16S ribosomal RNA (rRNA) gene of the bacterial community in the hindgut of R. virginicus was performed on termites exposed to chitosan treatment. Light microscopy visualization of protist species residing in the hindgut of workers showed presence of ten protist species both in the control sample and in termites fed a low concentration of chitosan. In this study, the coexistence of two species of the genus Trichonympha (T. agilis and T. burlesquei) is reported for the first time in R. virginicus. Monocercomonas sp. and Trichomitus trypanoides were the only two protists found in termites exposed to wood treated with higher chitosan concentration solutions and the absence of wood fragments in their food vacuoles was clear. This feature indicates that these two protists may not be involved in the digestion of the wood fragments impregnated with chitosan. The results of this study indicated that the potential effect of chitosan caused elimination of the protist species in termite hindguts. The genomic DNA of bacterial hindgut community of R. virginicus were profiled using sequences which amplified theV3-V4 sub-regions of 16S rRNA gene. Sequences were analyzed using a taxonomic analysis tool, Quantitative Insights Into Microbial Ecology (OIIME 2), in order to infer the effect of chitosan on the composition of the bacterial fauna in the hindgut. The richness and evenness results indicated that the most diversity was observed in the bacteria from termites not being exposed (UNX) to treatment compared to other treatment groups. On the other hand, the lowest richness and evenness were determined for chitosan-treated wood (CTE) and starved termites (STV). Of 28 bacterial phyla, Bacteroidetes, Firmicutes, Elusimicrobia, and Proteobacteria were the most dominant phyla across all the treatment groups. The results suggest that chitosan treated wood led to the microbial community shifts in R. virginicus. In addition, lack of a nutrition source and other changes in termite’s food affect the termite hindgut bacterial diversity.

The purpose of this study was to examine the direct and indirect effects of ultraviolet-B (UV-B) radiation on freshwater protists. Laboratory experiments were conducted in order to determine the importance of photoenzymatic repair (PER) of UVBinduced DNA damage in the heterotrophic nanoflagellate Paraphysomonas sp. Investigations into the combined effects of UV-B and chromophoric dissolved organic matter (CDOM) were conducted in laboratory experiments in which protist cultures were exposed to UV-B radiation in the presence and absence of water amended to a higher CDOM concentration in order to determine the ability of CDOM to act as a UV-B filter and as a potential nutrient source. Field experiments examined the responses of natural communities of protists and bacteria to ultraviolet radiation (UVR) in the presence of high and low concentrations of CDOM. Ultraviolet-B radiation (UV-B; 280 – 320 nm) negatively affects many aquatic organisms, including heterotrophic flagellates, by directly damaging DNA. The quantity of UV-B reaching the surface of a lake varies with atmospheric chemistry, including stratospheric ozone, and the presence of large holes (Alldredge 1977) in this ozone shield during the last decade resulted in historically high UV-B levels. In aquatic systems, the nature of the damage to organisms depends on the intensity and duration of solar radiation, plus its attenuation in the water column. The amount of UV-B damage is highly dependent on the concentration of CDOM in the water column because CDOM strongly absorbs UV-B radiation. This protective role of CDOM is likely to be reduced in areas where warmer, drier climate decreases watershed runoff, which ultimately results in acidification and increased CDOM photodegradation. However, CDOM also may also act as an organic carbon source for bacteria and stimulate growth of the microbial food web, including bacterivores like heterotrophic flagellates. The effect of UV and CDOM interactions on the microbial food web is not well understood, but climate-related increase in CDOM in an oligotrophic lake could increase the heterotrophic microbial food web impact by reducing UV-B damage and increasing available resources. Since aquatic organisms, including protists, are differentially susceptible to UV-B radiation, climate change effects on CDOM and UV-B attenuation are likely to alter the ecology and community structure of aquatic systems. This thesis describes investigations into the direct and indirect effects of UV-B radiation on freshwater protozoa. The role of PER of direct UV-B induced DNA damage was examined in laboratory experiments that compared the survival and population growth of the heterotrophic nanoflagellate Paraphysomonas sp. at two environmentally relevant temperatures. The results from these experiments demonstrated the reliance of Paraphysomonas sp. on PER, with 100% mortality in the absence of the photorepair radiation that activates photoenzymatic repair enzymes. The ability of Paraphysomonas sp. to recover from exposure to UV-B radiation declined in flagellates adapted to 15°C relative to the same exposures at 20°C. Experiments examining the direct and indirect effects of UV-B radiation and CDOM on freshwater protists conducted in the laboratory and in an oligotrophic lake in the Pocono Mountains showed that potential DNA damage resulting from UV exposure is reduced and microbial growth may be enhanced with an increase in CDOM concentration. / Biology

La diversité des protistes marins planctoniques, après avoir été historiquement étudiée sur des critères morphologiques, est depuis récemment sujette à une intense recherche à l’aide d’approches moléculaires. Notamment, les études basées sur l’amplification directe de marqueurs moléculaires à partir d’ADN environnemental ont révélées une exceptionnelle diversité. L’objectif central de ce travail est d’améliorer notre compréhension sur le lien existant entre la connaissance classique des eucaryotes unicellulaires et leur diversité estimée à partir des données moléculaires, en particulier pour une meilleure interprétation des processus évolutifs et écologiques. Pour cela, nous avons utilisé comme système modèle l’ordre des ciliés tintinnidés (Tintinnida) qui constituent un groupe riche en espèces, aisément identifiables au microscope grâce à leur coquille externe (lorica) et communément rencontrés dans l’ensemble des eaux marines et lacustres du monde. Un suivi approfondi sur deux ans des tintinnidés de la Baie de Villefranche-sur-Mer (Mer Méditerrannée, France), couplant des analyses moléculaires de la diversité à partir de cellules individuelles et à partir d’ADN environnemental, a permis de caractériser la composition de ces communautés et leur dynamique temporelle aux échelles macro- et micro-évolutives. La première partie de ce travail a été destinée à la réalisation d’une phylogénie moléculaire de référence pour les tintinnidés en incorporant les séquences de 62 individus de morphologies diverses pour lesquelles des données moléculaires n'étaient pas disponibles. Nous avons amplifié et séquencé les gènes codant pour les ARN ribosomiques (ARNr 18S, 5.8S et 28S) et les espaces intergéniques correspondants (ITS1 et ITS2). La classification taxonomique a été réévaluée d’après les données moléculaires. Dans un deuxième temps, nous avons testé l’efficacité des approches moléculaires conventionnelles (amplification, clonage et séquençage Sanger du gène de l'ARNr 18S) et plus récentes (amplification et pyroséquençage de régions de l'ARNr 18S et de l’ITS), pour décrire la composition des communautés des tintinnidés dans des échantillons environnementaux en les comparant avec des estimations de la diversité par observation morphologique sur les mêmes échantillons. Si il existe de légères incongruences entre les approches et/ou les différents marqueurs employés, les approches cultureindépendantes s’avèrent efficaces pour décrire la diversité morphologique. En revanche, afin de ne pas surévaluer artificiellement le nombre d’espèces estimées à partir des données de pyroséquençage, il faut que des méthodes de débruitage et de regroupement en unités taxonomiques opérationnelles (UTOs) contraignantes soient appliquées. La troisième partie de ce travail a été dédiée au suivi temporel des communautés de tintinnidés à différentes profondeurs dans la baie de Villefranche, basé sur le clonage et le séquençage du gène de l'ARNr 18S et des régions ITS. Il apparaît des différences de distribution au cours de l’année à une même profondeur, en particulier en termes d’abondance de séquences pour une UTO donnée. Malgré un cadre phylogénétique solide et assez enrichi, l’approche moléculaire révèle des séquences éloignées des espèces déjà séquencées. La découverte de ces clades environnementaux souligne potentiellement l’importance écologique d’espèces encore mal connues. Enfin, le séquençage direct du gène de l'ARNr 18S et de l'ITS2 à partir des cellules individuelles de l'espèce <Undella claparedei> a offert l’opportunité d’une étude populationnelle sur une période de deux ans. La diversité intra-spécifique mesurée met à jour des phénomènes d’hybridation entre variantes génétiques. Une structuration génétique temporelle a également été observée pour le gène de l'ARNr 18S. Les implications de ces différentes recherches sont discutées dans le cadre de l’étude de la diversité et de l’écologie des tintinnidés, et plus largement, des protistes marins. / The marine protistan diversity has been historically studied based on morphological characterization but has recently been the object of intense research using molecular approaches. Studies based on the amplification of molecular markers from environmental DNA revealed an outstanding diversity, partly new and uncharacterized. However, the actual extent of this diversity remains poorly known and highly debated. The main goal of this work was to improve our knowledge on protistan diversity to bridge the gap between molecular environmental surveys and classical protistology to better understand the ecology and evolution of unicellular eukaryotes. For this purpose, we used as a model the species-rich order of the tintinnid ciliates (Tintinnida, Ciliophora), which are easily distinguishable because of their secreted shell, the lorica, and commonly found in marine waters all around the globe. A two-year monitoring of the tintinnid populations in the Bay of Villefranche-sur- Mer (Mediterranean Sea, France), combining molecular analyses of the diversity based on single-cells and environmental DNA, gave us the opportunity to describe the tintinnid community composition and its temporal dynamics. In the first part of this work, we constructed a reference molecular phylogeny for the tintinnids including new sequences from 62 specimens of diverse morphologies, for which we amplified and sequenced the ribosomal coding genes (18S, 5.8S and 28S rRNA) and the corresponding intergenic spacers (ITS1 and ITS2). The taxonomic classification of the Tintinnida has been revised based on these molecular data. In the second part, in order to assess the accuracy of molecular-based approaches to describe the natural species assemblages of tintinnids, we compared the morphology-based diversity estimates with those derived from classical (amplification, cloning and Sanger sequencing of the 18S rRNA gene) and more recent (direct pyrosequencing of amplified 18S rRNA genes and ITS regions) molecular approaches. Even if there are still some disagreements between the different methods and/or molecular markers, the culture-independent approaches were efficient to describe the morphological diversity. However, a careful and rigorous analysis of pyrosequencing datasets, including sequence denoising and stringent sequence clustering in Operational Taxonomic Units (OTUs) with well-adjusted parameters, is necessary to avoid overestimating the species number. The third part of the thesis is dedicated to the study of the genetic diversity of tintinnids over a one-year survey in the Bay of Villefranche at five different depths by combining community fingerprinting analysis using denaturing gradient gel electrophoresis (DGGE) with direct PCR amplification and sequencing of 18S, 5.8S, and 28S rRNA genes and ITS regions. These analyses revealed marked seasonal changes, in particular in the sequence abundances of certain OTUs. In addition, despite an enriched phylogenetic reference sequence dataset for the tintinnids, we retrieved two abundant phylotypes without any closely related known species, highlighting the possible ecological relevance of unidentified species. Finally, we studied the intra-specific diversity of populations of the species <Undella claparedei> based on 18S rDNA and ITS direct sequencing of single-cells collected over a period of two years. We detected signals of hybridization and sexual recombination among different genetic variants. We also found genetic structuring of the 18S rRNA gene data differentiating populations collected at different times. The implications of all these results are discussed in the framework of the diversity and ecology of tintinnid ciliates and, more generally, of marine protists