This thesis contributes to the development of dinoflagellate cysts as indicators of past environmental change in the Northeastern Pacific coastal ocean, and investigates past variations in sea-surface temperature, salinity and primary productivity encoded in dinoflagellate cyst sedimentary records from the Santa Barbara Basin (SBB, southern California) and Effingham Inlet (Vancouver Island, British Columbia) over the last millennium. The dinoflagellate cyst records extracted from the SBB and Effingham Inlet predominantly laminated sediments and analysed at sub-decadal resolutions, constitute some of the most detailed records of cyst-producing dinoflagellate populations in the world. A two year-long sediment trap study from the SBB documents the seasonality in dinoflagellate cyst production for the first time on the Pacific coast of the United States. The study shows that dinoflagellate cyst data can be used as indicators of changes in sea-surface temperature and primary productivity associated with seasonal upwelling in the SBB. In particular, several dinoflagellate cyst taxa such as Brigantedinium spp. and Lingulodinium machaerophorum are identified as indicators of “active upwelling” (typically occurring in spring and early summer) and “relaxed upwelling” conditions (fall and early winter) at the site, respectively. Analysis of a dinoflagellate cyst record from the SBB spanning the last ~260 years at biannual resolution documents the response of cyst-producing dinoflagellates to instrumentally-measured warming during the 20th century, and reveals decadal scale variations in primary productivity at the site that are coherent with phases of the Pacific Decadal Oscillation (PDO). The cyst assemblages are dominated by cysts produced by heterotrophic dinoflagellates (in particular Brigantedinium spp.), but the turn of the 20th century is marked by an abrupt increase in concentrations of L. machaerophorum and Spiniferites ramosus, two cyst taxa of autotrophic affinity. Their increasing abundances during the 20th century are interpreted to reflect warmer conditions and possibly stronger stratification during summer and fall. The dinoflagellate cyst data suggest a warming pulse in the early 1900s and provide further evidence that persistently warmer and/or more stratified conditions were established by the late 1920s. The dinoflagellate cyst record from Effingham Inlet, spanning the last millennium, is characterized by the proportionally equal contribution of cysts produced by autotrophic and heterotrophic dinoflagellates in most samples. The cyst data indicate variations in sea-surface temperature, salinity and primary productivity that are associated with local expressions of the Medieval Climate Anomaly (from the base of the record to ~1230), the Little Ice Age (from ~1230 to ~1900) and warming during the second half of the 20th century. Both dinoflagellate cyst records reveal that since the beginning (in the SBB) and mid-20th century (in Effingham Inlet), autotrophic dinoflagellates contribute to a greater portion of the primary production in the region, whereas heterotrophic dinoflagellates, as indicators of diatom populations, decline. Variability in the dinoflagellate cyst data is coherent at both sites and suggest a reduced expression of decadal scale variability associated with the PDO during the 19th century. / Graduate / 0416 / 0427 / mbringue@uvic.ca

During the Late Pliocene, between 3.3 Ma and 2.6 Ma, tectonic events changed ocean basin interactions against a background of shifting orbital forcing mechanisms and a global cooling trend. A climate system that had been locked in a stable, warm state gradually transformed into one typified by the high-amplitude glacial–interglacial fluctuations characteristic of the later Quaternary. The onset of Northern Hemisphere glaciations in the Late Pliocene marks an important step in this transition, due to the role of feedback mechanisms including ice albedo. A crucial factor in this Northern Hemisphere ice sheet expansion is the North Atlantic surface ocean circulation. To evaluate how they are linked, a ca. 200-kyr time slab spanning 2782-2520 ka (Late Pliocene–Early Pleistocene) was analyzed at millennial scale resolution from eastern North Atlantic Deep Sea Drilling Project (DSDP) Site 610 and Integrated Ocean Drilling Program (IODP) Site U1313. The causes of the Plio-Pleistocene climatic turnover are compared to that of the well-documented Marine Isotope Stage (MIS) M2 occurring in the Late Pliocene (3.3 Ma). MIS M2, a severe glacial event seen as a precursor to later Quaternary-style glaciations, was investigated from western North Atlantic DSDP Site 603. Utilizing a same-sample methodology, two paleoceanographic proxies were used: (1) dinocyst assemblages, and (2) foraminiferal geochemistry (δ18O and Mg/Ca). Dinocysts are proven tracers of sea-surface temperature (SST), salinity, nutrient supply, and sea ice cover, and are analyzed here to characterize the overlying water masses at the studied sites. Strong dinocyst assemblage fluctuations attest to variations in the influence of the North Atlantic Current (NAC). Using Mg/Ca ratios for the planktonic foraminifer Globigerina bulloides to determine absolute SSTs allows salinity changes to be reconstructed when combined with stable oxygen isotopes. This study shows a persistent Gulf Stream–NAC in the western North Atlantic during MIS M2, favoring a southern shift of the NAC over a shutdown of the thermohaline circulation. At the newly established Plio-Pleistocene boundary, a profound turnover in dinoflagellate cyst assemblages reveals a shift in ocean mode during MIS 104 (2.6 Ma). Three distinct dinocyst ecozones demonstrate this fundamental reorganization of the North Atlantic circulation.

タンデトロン加速器質量分析計業績報告

(Bahasa Indonesia) Analisa yang terperinci mengenai lingkungan di masa lalu, iklim dan sejarah penggunaaan lahan di wilayah Indonesia sangat penting untuk memperoleh pemahaman yang lebih baik mengenai hubungan manusia-lingkungan dan untuk mencegah ketidakpastian perkembangan wilayah tersebut di masa depan. Indonesia merupakan salah satu wilayah yang memiliki keanekaragaman terbesar, dan pada saat yang bersamaan juga merupakan salah satu Negara yang mempunyai jumlah penduduk terpadat di dunia. Seiring dengan sejarah, pengaruh dari aktivitas manusia pada suatu daerah menjadi semakin kuat. Penelitian ini dilakukan untuk mengakses peranan manusia terhadap perubahan lingkungan. Penelitian kami difokuskan pada rekonstruksi pola vegetasi di masa lampau, perubahan lingkungan dan interaksi antara manusia dan lingkungan yang tercermin dalam sedimen laut di perairan Indonesia. Dua macam pendekatan yang digunakan dalam studi ini adalah: polen (serbuik sari), yang berasal dari darat dan diharapkan bisa memberikan informasi yang beragam tentang vegetasi dan dinamika penggunaan lahan, dan organic dinoflagelata yang berasal dari lingkungan laut dan merefleksikan perubahan parameter air secara kuantitatif (misal. SST, SSS) dan kualitatif (mis: kondisi tropic dilihat dari segi makro-elemen utama dan oksigen terlarut dalam air). Selain itu, arang mikro dipelajari untuk mendapatkan data mengenai sejarah kebakaran di wilayah tersebut dan untuk memperoleh data tambahan untuk interpretasi polen dan data dinoflagelata. Penelitian dilakukan di dua situs sebagai perbandingan: pertama, di wilayah Jawa yang padat penduduk dengan sejarah panjang dari dampak aktivitas manusia yang menghasilkan lanskap pertanian yang luas, dan yang kedua, di wilayah Kalimantan Selatan dengan kepadatan penduduk yang tidak terlalu tinggi dan tidak banyak perubahan akibat pengaruh aktivitas manusia dan masih merupakan vegetasi alami. Metode yang digunakan, palinologi laut memerlukan perhatian khusus dalam interpretasi data. Faktor pengendapan polen adalah sangat penting, terutama untuk daerah-daerah dengan pengaruh kuat dari angin dan arus laut seperti wilayah Indonesia dimana sistem iklim secara keseluruhan didorong sebagian oleh pergantian musim. Untuk mendapatkan beberapa pemikiran mengenai transportasi sedimen di wilayah ini, kami mempelajari dan membahas secara rinci perbedaan jumlah polen yang dikumpulkan pada kondisi musim hujan yang berbeda serta selama waktu perpindahan musim. Subyek manuskrip pertama kami adalah kemelimpahan dan komposisi taksa modern polen dan spora yang didapat dari sedimen yang terakumulasi di Samudera India sebelah barat daya Jawa. Hasil yang diperoleh digunakan untuk interpretasi lebih lanjut dari fosil polen laut. Sejarah intensifikasi penggunaan lahan dan perubahan vegetasi lebih dari 3500 tahun yang lalu yang diperoleh dari dinoflagelata dan kumpullan polen dari sedimen laut dipresentasikan dalam jurnal yang kedua. Studi ini didasarkan pada perbandingan dua core laut dari lepas Laut Jawa dekat Kalimantan Barat (Sungai Jelai) and bagian timur laut Jawa (Sungai/Bengavan Solo). Pada manuskrip yang ketiga, hasil ini diperbandingkan dengan sedimen core dari lepas pantai yang diambil dari bagian hulu sungai Pembuang. Studi ini membahas mengenai hasil analisa geokimia dan analisa dinoflagelata dalam cakupan paleoekologi dan paleoenvironment. Manuskrip kelima membahas tentang keragaman polen dalam core sedimen laut dari wilayah Indonesia. Studi ini merangkum pengetahuan yang diperoleh selama meneliti core sedimen dari Laut Jawa dan dari studi perangkap sedimen di Samudera Hindia. Dalam bentuk atlas polen, kami memberikan hasil analisis secara rinci dari daftar taksa polen dan dilengkapi dengan foto mikro pada tingkat fokus yang berbeda. Hasil keseluruhan dari penelitian ini akan memberikan kontribusi pada pengetahuan tentang dinamika ekosistem dan sejarah alam di wilayah Indonesia dan dapat membantu investigasi paleoekologi dan paleo-iklim di masa depan secara lebih rinci.

Knowing the taxonomy of unicellular dinoflagellate cysts is important in reconstructing paleoenvironments, paleoclimatology and paleobathymetry. Different dinoflagellates tend to prefer different depths, salinity levels and climate. Species of dinocysts only occur during a certain interval in the geological record and are therefore an important tool for dating sediments. Biostratigraphic research uses age determination of sediments depending on first and last occurrences of different species, or co-occurrences of several species. However, it can be rather time consuming and difficult to identify dinoflagellate cysts for people that are not experts in this field. In an attempt to resolve this, a database was created for 145 genera of dinoflagellate cysts existing during Palaeocene and Eocene in the online accessible program Xper3. Morphological criteria or “descriptors” were added along with describing “states”. The number ofmorphological descriptors chosen were 13, with 3 to 15 states for each descriptor.Each genus was described in a matrix and was given one or more unique states for each descriptor, which were defined from the literature by original morphological descriptions of dinocyst genera and photographs of holotypes. A morphological identification key was automatically created in Xper3 from this database, which enabled identification of genera by choosing unique states that were visible for the dinocysts being analysed.A test using photographs with different levels of preservation of dinoflagellate cysts of Eocene age of Aquitaine basin was undertaken in order to assess the reliability of the morphological identification key. The aim was also to see which morphological criteria were more common and how many descriptors and states were needed to reach an end-result of 5 remaining genera, including the correct genus.Errors that were caused in the identification key were immediately reviewed and re-tested. In 38 of 43 tries, a maximum of five genera were remaining, with the correct genus included. This confirmed that the identification key worked relatively well.Another test demonstrated how the identification key worked for identifying dinocysts with an optical microscope in unknown samples, which are photographed and published in the present report, along with data showing how many descriptors and states were used, remaining genera and which states were chosen for each genus.In general, only 1-8 descriptors were necessary and 5 the most common number used. The morphological character (state) “type of ornamentation” was the most widely used followed by “distribution of ornamentation”, “shape of the cyst” and “size of the ornamentation”. However, the archeopyle (excystment opening), was not always visible in the dinocysts, but is still considered a key morphological descriptor. / Dinoflagellater är en typ av mikroskopiska plankton som kan bilda så kallade cystor eller vilosporer för att skydda sig vid kritiska miljöförändringar. Dessa cystor kan ligga vilandes i sediment under en längre tid. Det är också dessa cystor som bevaras som fossil. Eftersom det finns en sådan hög mångfald av dinoflagellatcystor i fossila sediment, liksom att de mikroskopiska, existerar över stora delar av jorden samt att de har en snabb evolution, så används de ofta till att datera sediment inom biostratigrafi.För att kunna datera sediment med hjälp av dinoflagellatcystor, krävs det att man kan identifiera de olika arterna och veta i vilken tidsålder de existerade. Att klassificera dinoflagellatcystor kan därför vara mycket svårt och ta en hel del tid om man inte är någon expert. I denna studie har därför en databas och identifieringsnyckel skapats i ett onlinebaserat dataprogram kallat Xper3. Xper3 är primärt riktat till att hjälpa personer med grundläggande kunskaper i att beskriva utseendemässiga karaktärer hos olika typer av mikrofossil, inklusive dinoflagellatcystor.I denna identifieringsnyckel använde jag mig av 145 olika dinoflagellatsläkten vilka alla existerade någon gång under tidig Paleogen, dvs hela Paleocen och/eller Eocen (66–34 miljoner år sedan). Dessutom användes 13 olika morfologiska beskrivningar ”descriptors” med 3–15 olika svar ”states” per beskrivning.Målet är att få en identifieringsnyckel som unikt kan identifiera olika typer av dinoflagellatcystor på genusnivå, med ett förslag på maximalt fem återstående släkten (genera). Studien undersökte även vilka morfologiska beskrivningar som är mest användbara och hur många olika typer av beskrivningar som behövs för att analysera dinoflagellatcystor.För att testa om identifieringsnyckeln fungerade, användes olika typer av kända och okända dino-flagellatcystor i ett så kallat ”Test 1: Kända dinoflagellatcystor” och ”Test 2: Okända dinoflagellat-cystor.I det första testet, ”Test 1”, grupperades kända dinoflagellatcystor i olika typer av bevarande tillstånd så som ”välbevarade”, ”tveksamt bevarande” och ”väldigt dåligt bevarade” dinoflagellat-cystor. Detta test förde statistik på hur många släkten av förslag som kom upp i slutändan och vilka morfologiska beskrivningar som användes mest och hur många olika beskrivningar som behövdes.Det andra testet, ”Test 2”, undersökte hur denna identifieringsnyckel fungerade att analysera dinoflagellatcystor från okända prover under mikroskop. Fotograferade dinoflagellatcystor presente-rades i denna rapport tillsammans med detaljer på hur de hade identifierats.I de flesta fallen, kunde identifieringsnyckeln ge ett förslag på maximalt fem återstående släkten av dinoflagellatcystor, där det korrekta släktet var ett utav förslaget, vilket tyder på att identifierings-nyckeln fungerar. Den mest använda morfologiska beskrivningen var ”typ av ornament”, och antal morfologiska beskrivningar som behövdes var mellan ett till åtta, där fem var det antal beskrivningar som mest användes i att identifiera dinoflagellatcystor i identifieringsnyckeln.

During the Late Pliocene, between 3.3 Ma and 2.6 Ma, tectonic events changed ocean basin interactions against a background of shifting orbital forcing mechanisms and a global cooling trend. A climate system that had been locked in a stable, warm state gradually transformed into one typified by the high-amplitude glacial–interglacial fluctuations characteristic of the later Quaternary. The onset of Northern Hemisphere glaciations in the Late Pliocene marks an important step in this transition, due to the role of feedback mechanisms including ice albedo. A crucial factor in this Northern Hemisphere ice sheet expansion is the North Atlantic surface ocean circulation. To evaluate how they are linked, a ca. 200-kyr time slab spanning 2782-2520 ka (Late Pliocene–Early Pleistocene) was analyzed at millennial scale resolution from eastern North Atlantic Deep Sea Drilling Project (DSDP) Site 610 and Integrated Ocean Drilling Program (IODP) Site U1313. The causes of the Plio-Pleistocene climatic turnover are compared to that of the well-documented Marine Isotope Stage (MIS) M2 occurring in the Late Pliocene (3.3 Ma). MIS M2, a severe glacial event seen as a precursor to later Quaternary-style glaciations, was investigated from western North Atlantic DSDP Site 603. Utilizing a same-sample methodology, two paleoceanographic proxies were used: (1) dinocyst assemblages, and (2) foraminiferal geochemistry (δ18O and Mg/Ca). Dinocysts are proven tracers of sea-surface temperature (SST), salinity, nutrient supply, and sea ice cover, and are analyzed here to characterize the overlying water masses at the studied sites. Strong dinocyst assemblage fluctuations attest to variations in the influence of the North Atlantic Current (NAC). Using Mg/Ca ratios for the planktonic foraminifer Globigerina bulloides to determine absolute SSTs allows salinity changes to be reconstructed when combined with stable oxygen isotopes. This study shows a persistent Gulf Stream–NAC in the western North Atlantic during MIS M2, favoring a southern shift of the NAC over a shutdown of the thermohaline circulation. At the newly established Plio-Pleistocene boundary, a profound turnover in dinoflagellate cyst assemblages reveals a shift in ocean mode during MIS 104 (2.6 Ma). Three distinct dinocyst ecozones demonstrate this fundamental reorganization of the North Atlantic circulation.

Heteromorph ammonites and dinoflagellate cysts from the Upper Cretaceous Northumberland Formation on Hornby Island, British Columbia, Canada are examined. The collection and preparation of new material has enabled the recognition of eleven species of which only three have been reported from the locality. Of these taxa represented from three heteromorph ammonite families in the study area, five are new occurrences and three are new to science. This expansion of the Hornby Island ammonite fauna is presented alongside a pioneering taxonomic survey of dinoflagellate cysts from the same rocks. Together, these macro- and microfossils reinforce a late Campanian age for the Northumberland Formation with the upper extent of the section approaching the Campanian-Maastrichtian boundary (CMB) interval. The palaeoecology and evolutionary relationships of these heteromorph ammonoids are considered with new insights into their ontogenetic development and neritic palaeoenvironmental circumstances. The dinoflagellate cysts and associated terrestrial palynomorphs have also allowed for enhanced palaeoenvironmental reconstruction and depositional setting inference. The scope of the studied material, and the presence of key index taxa, enables refined biostratigraphy and a stronger basis for correlation of the Hornby Island succession with neighboring coeval biotic provinces. / Graduate / 2018-08-10

The central objective of this study is to understand phytoplankton community response following the global mass extinction event at the Cretaceous–Paleogene (K/Pg) boundary. The objective is approached through analysis of dinoflagellate cyst assemblages across the boundary interval in the North Pacific. Dinoflagellate cysts are powerful tools for deep time paleoenvironmental reconstructions and this group of microfossils has been vastly underutilized in this region of the world. On this premise, comprehensive marine palynological surveys were undertaken for the Oyster Bay Formation of eastern Vancouver Island, British Columbia, Canada and Shatsky Rise in the northwest Pacific. The Oyster Bay Formation work resulted in the discovery of the first K/Pg boundary succession west of the Rocky Mountains based on biostratigraphic controls and refined taxonomy for the genus Cannosphaeropsis found within these strata. Three new taxa are described: Cannosphaeropsis franciscana subsp. vacuoseptata subsp. nov., Cannosphaeropsis franciscana subsp. vesiculata subsp. nov. and Phelodinium fensomei sp. nov. The cyst assemblages reveal endemic associations and signals of transition between offshore coastal to estuarine settings in keeping with global eustatic trends. Oyster Bay Formation results and interpretations are compared to analyses of core samples from Deep Sea Drilling Project Site 577 at Shatsky Rise. Contrast is seen between a diverse, highly productive coastal to estuarine environment in the Oyster Bay Formation as represented by organic-walled taxa and an oligotrophic bathyal environment at Shatsky Rise during the same interval as represented by a small number of calcareous taxa. These two regions form the basis for comparison between differing assemblages in order to ascertain the extent to which phytoplankton communities were affected by changes in sea-surface and water mass conditions in conjunction with the K/Pg event. The findings reveal measurable impacts of climate and paleoenvironmental change reflected by shifts in assemblage composition and cyst morphology. A lack of extinction among many forms is consistent with studies from around the globe as presented in an exhaustive review of the literature. The dinoflagellates were marginally impacted with the most specialized taxa presenting a record of sea-surface temperature fluctuation, nutrient supply and opportunistic niche exploitation. / Graduate / 2022-08-20

Les urgences écologiques actuelles, résultant des dérives de l'industrialisation et de la mondialisation, mènent la recherche fondamentale à se préoccuper hâtivement de la biologie de certains organismes comme les dinoflagellés. Ces organismes sont à la base de la chaîne alimentaire, et certaines espèces sont impliquées dans la formation des récifs coralliens. De plus, la prolifération incontrôlée de certaines espèces de dinoflagellés engendrée par l'eutrophisation industrielle est responsable des marées rouges qui menacent d'une part la flore et la faune aquatiques. Certaines des toxines produites par ces efflorescences algales ont un effet sur la santé publique, car elles peuvent rendre dangereuse la consommation alimentaire de poissons ou de fruits de mer contaminés. Nous avons examiné le comportement de l’espèce Lingulodinium polyedra à travers des cycles diurnes. Dans un premier projet, le protéome dans des extraits d'algues récoltés sur un cycle de 24 heures en conditions de 12 heures de jour suivies de 12 heures de nuit (un cycle LD) a été examiné. Nous avons identifié treize protéines clés qui ont montré des variations quantitatives synchronisées avec les temps de réalisation des rythmes biologiques les impliquant. Deux protéines déjà connues de varier faisait partie de ce groupe, tandis que les autres protéines sont impliquées dans des processus rythmiques nouveaux. Nous avançons l’hypothèse qu’une augmentation quantitative des protéines clés permettrait à l'accomplissement des différents processus cellulaires à différents moments de la journée. Dans un second projet, nous avons examiné la vitesse de synthèse des protéines qui pourrait expliquer ces variations quantitatives protéiques. En appliquant la technique du profilage ribosomal ( « ribosome profiling ») sur des échantillons algaux collectés d’abord à trois temps, puis ensuite sur tout le cycle LD, nous avons confirmé des variations de vitesse de synthèse des protéines identifiées dans notre étude protéomique et des protéines dont la vitesse de synthèse a déjà été mesurée par l’incorporation de méthionine radioactive in vivo. De plus, nous avons identifié plusieurs milliers d’autres séquences dont la vitesse de synthèse varie. Une classification des séquences dans les catégories GO nous a permis d’identifier un rythme diurne dans la synthèse des acides aminés qui pourrait aider à comprendre le métabolisme du nitrate. Nous proposons que des variations de vitesse de synthèse entraînent des augmentations quantitatives des protéines aux niveaux inférieurs à ce que l’on a pu détecter par la spectroscopie de masse. La variation dans les niveaux de protéines clés pourrait aider l'accomplissement des rythmes diurnes chez le dinoflagellé Lingulodinium. Ces avancées dans la compréhension de la régulation des rythmes biologiques du dinoflagellé Lingulodinium d'une part permettront de mieux penser la recherche concernant la lutte écologique contre les marées rouges et d'autre part ouvriront de nouvelles perspectives dans l'entendement de la régulation des rythmes biologiques des autres organismes y compris ceux de l'Homme dont les troubles impliquent de nombreuses maladies. / Industrialization and globalization has led to industrial eutrophication in many regions of the oceans resulting in different types of ecological emergencies. One of these is the uncontrolled proliferation of dinoflagellates which are responsible for the harmful algal blooms called “red tides”. Certain species release toxins which can harm aquatic flora and fauna and, through consumption of contaminated fish or seafood, can affect public health. Dinoflagellates are also at the base of the food chain in the marine environment, and certain species form symbioses with anthozoans thus allowing growth of coral reefs. There is thus a strong need for fundamental research on dinoflagellate biology. Using the dinoflagellate Lingulodinium polyedra as a model, we have examined how cells adapt to the daily changes in light and dark. In particular we have examined changes in protein amounts as well as changes in protein synthesis rates to gain insight into how cells differ during the day and night. In a first project, the daily proteome was examined by mass spectrometry using algae extracts harvested over a 24 hour cycle in conditions of 12 hours of day followed by 12 hours of night. Key proteins involved in biological rhythms have shown quantitative variations synchronized with the times of the biological rhythms involving them, ie a quantitative increase in key proteins is necessary for the accomplishment of the various cellular processes. Thirteen proteins were identified, of which two were previously documented to change in amount over the daily cycle. In a second project we addressed the origin of these quantitative protein variations. By applying the technique of ribosome profiling on algal samples, first collected in triplicate at three times and then at two hour intervals throughout the 24 h cycle, we have identified iv variations in the synthesis rate of thousands of proteins. These include the proteins found in the proteomic analysis as well as four proteins whose synthesis rate variations had already been observed using in vivo metabolic labeling. Interestingly, classification of the regulated proteins into GO categories also revealed a late night increase in the synthesis of many amino acid biosynthetic enzymes, potentially linking amino acid synthesis associated with the daily metabolism of nitrate. These advances in our understanding of the regulation of the daily rhythms of the dinoflagellate Lingulodinium will provide new tools in the ecological fight against red tides. They may also open new perspectives in understanding the daily rhythms of other organisms.

Les dinoflagellés sont des eucaryotes unicellulaires que l’on retrouve autant en eau douce qu’en milieu marin. Ils sont particulièrement connus pour causer des fleurs d’algues toxiques nommées ‘marée-rouge’, ainsi que pour leur symbiose avec les coraux et pour leur importante contribution à la fixation du carbone dans les océans. Au point de vue moléculaire, ils sont aussi connus pour leur caractéristiques nucléaires uniques, car on retrouve généralement une quantité immense d’ADN dans leurs chromosomes et ceux-ci sont empaquetés et condensés sous une forme cristalline liquide au lieu de nucléosomes. Les gènes encodés par le noyau sont souvent présents en multiples copies et arrangés en tandem et aucun élément de régulation transcriptionnelle, y compris la boite TATA, n’a encore été observé. L’organisation unique de la chromatine des dinoflagellés suggère que différentes stratégies sont nécessaires pour contrôler l’expression des gènes de ces organismes. Dans cette étude, j’ai abordé ce problème en utilisant le dinoflagellé photosynthétique Lingulodinium polyedrum comme modèle. L. polyedrum est d’un intérêt particulier, car il a plusieurs rythmes circadiens (journalier). À ce jour, toutes les études sur l’expression des gènes lors des changements circadiens ont démontrées une régulation à un niveau traductionnel. Pour mes recherches, j’ai utilisé les approches transcriptomique, protéomique et phosphoprotéomique ainsi que des études biochimiques pour donner un aperçu de la mécanique de la régulation des gènes des dinoflagellés, ceci en mettant l’accent sur l’importance de la phosphorylation du système circadien de L. polyedrum. L’absence des protéines histones et des nucléosomes est une particularité des dinoflagellés. En utilisant la technologie RNA-Seq, j’ai trouvé des séquences complètes encodant des histones et des enzymes modifiant les histones. L polyedrum exprime donc des séquences conservées codantes pour les histones, mais le niveau d’expression protéique est plus faible que les limites de détection par immunodétection de type Western. Les données de séquençage RNA-Seq ont également été utilisées pour générer un transcriptome, qui est une liste des gènes exprimés par L. polyedrum. Une recherche par homologie de séquences a d’abord été effectuée pour classifier les transcrits en diverses catégories (Gene Ontology; GO). Cette analyse a révélé une faible abondance des facteurs de transcription et une surprenante prédominance, parmi ceux-ci, des séquences à domaine Cold Shock. Chez L. polyedrum, plusieurs gènes sont répétés en tandem. Un alignement des séquences obtenues par RNA-Seq avec les copies génomiques de gènes organisés en tandem a été réalisé pour examiner la présence de transcrits polycistroniques, une hypothèse formulée pour expliquer le manque d’élément promoteur dans la région intergénique de la séquence de ces gènes. Cette analyse a également démontré une très haute conservation des séquences codantes des gènes organisés en tandem. Le transcriptome a également été utilisé pour aider à l’identification de protéines après leur séquençage par spectrométrie de masse, et une fraction enrichie en phosphoprotéines a été déterminée comme particulièrement bien adapté aux approches d’analyse à haut débit. La comparaison des phosphoprotéomes provenant de deux périodes différentes de la journée a révélée qu’une grande partie des protéines pour lesquelles l’état de phosphorylation varie avec le temps est reliées aux catégories de liaison à l’ARN et de la traduction. Le transcriptome a aussi été utilisé pour définir le spectre des kinases présentes chez L. polyedrum, qui a ensuite été utilisé pour classifier les différents peptides phosphorylés qui sont potentiellement les cibles de ces kinases. Plusieurs peptides identifiés comme étant phosphorylés par la Casein Kinase 2 (CK2), une kinase connue pour être impliquée dans l’horloge circadienne des eucaryotes, proviennent de diverses protéines de liaison à l’ARN. Pour évaluer la possibilité que quelques-unes des multiples protéines à domaine Cold Shock identifiées dans le transcriptome puissent moduler l’expression des gènes de L. polyedrum, tel qu’observé chez plusieurs autres systèmes procaryotiques et eucaryotiques, la réponse des cellules à des températures froides a été examinée. Les températures froides ont permis d’induire rapidement un enkystement, condition dans laquelle ces cellules deviennent métaboliquement inactives afin de résister aux conditions environnementales défavorables. Les changements dans le profil des phosphoprotéines seraient le facteur majeur causant la formation de kystes. Les phosphosites prédits pour être phosphorylés par la CK2 sont la classe la plus fortement réduite dans les kystes, une découverte intéressante, car le rythme de la bioluminescence confirme que l’horloge a été arrêtée dans le kyste. / Dinoflagellates are unicellular eukaryotes found in both marine and freshwater environments. They are best known for causing toxic blooms called ‘red-tides’, for their symbiosis with corals, and for their important contribution to carbon fixation in the ocean. On a more molecular level, they are also known for their unique nuclear characteristics, as they generally have huge amount of DNA found in chromosomes that are permanently condensed and packaged into liquid crystalline forms instead of nucleosomes. Nuclear-encoded genes are often present in multiple copies and arranged in tandem, and no putative promoter elements including the conserved TATA box, have yet been observed. The unique organization of dinoflagellate chromatin suggests different strategies may be required to regulate gene expression in these organisms. In this study, I have started to address this problem using the photosynthetic dinoflagellate Lingulodinium polyedrum as a model. L. polyedrum is of particular interest because it shows a number of circadian (daily) rhythms. To date, all circadian changes in gene expression studied are regulated at a translational level. I have used transcriptomic, proteomic and phosphoproteomic approaches along with biochemical studies to provide insight into the gene regulatory mechanisms in dinoflagellates, with particular emphasis on the importance of phosphorylation in the L. polyedrum circadian system. The absence of histone proteins and nucleosomes is a hallmark of the dinoflagellates. Using high throughput RNA-seq technology, I found complete set of sequences encoding the core histones as well as sequences encoding histone-modifying enzymes in L. polyedrum. Thus L. polyedrum expresses conserved histone transcripts, although levels of proteins are still below what can be detected using immunoblotting studies. Using the de novo assembly algorithm the RNA-seq data was used to generate a transcriptome. This transcriptome, a list of genes expressed by L. polyedrum, has been extensively characterized. First, homology based sequence searches were used to classify the transcripts in gene ontology (GO) categories, and this analysis revealed a reduced number of transcription factor types and a surprising predominance of sequences containing a cold shock domain. Alignments of reads from the RNA–seq to genomic copies of L. polyedrum tandem repeat sequences was performed to assess the possibility of polycistronic transcripts, a hypothesis proposed to explain the lack of promoter elements in the intergenic region of the tandem repeat gene sequences. This analysis also showed a surprisingly high conservation of tandemly repeated gene sequences. The transcriptome database was also used to fuel gene identification after protein sequencing by mass spectrometry, and a purified phosphoproteome fraction was found to be particularly amenable to high throughput approaches. A comparison of the phosphoproteome at two different times of day revealed that a major class of proteins whose phosphorylation state varied over time belonged to the RNA binding and translation GO category. The transcriptome was also used to define the spectrum of kinases present in L. polyedrum, which in turn was used to classify the different phosphorylated peptides as potential kinase targets. Predicted peptides of casein kinase 2 (CK2), a kinase known to be involved in the circadian clocks of other eukaryotes, were found to include many RNA binding proteins. To assess the possibility that some of the many cold shock domain proteins identified in the transcriptome might modulate gene expression in L. polyedrum, as has been observed in many other eukaryotic and prokaryotic systems, the cellular response to cold temperatures was examined. Cold temperatures were found to induce rapid encystment, a metabolically inactive cell type whose role is to combat unfavourable environmental conditions. Changes in phosphoproteome profile were found to be the major molecular correlates to cyst formation. Predicted CK2 phosphosites are the most highly reduced class of kinase targets, a finding of interest as measurements of the bioluminescence rhythm confirmed that the clock is stopped in cysts