Thesis (Ph. D.)--Lehigh University, 1999. / Includes vita. Bibliography: leaves 94-102.

Thesis (doctoral)--Rijksuniversiteit Groningen, 1992. / Consists chiefly of 8 articles previously published in journals, 1979-1991. Some articles co-authored with other writers. "Stellingen" sheet inserted. Includes bibliographical references.

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 101-109). Also available on the World Wide Web.

Thesis (M.S.)--University of West Florida, 2006. / Title from title page of source document. Document formatted into pages; contains 110 pages. Includes bibliographical references.

Les diatomées jouent un rôle primordial dans l'écologie de la planète, car elles sont responsables du 20-40% de la productivite mondial d’oxygène. Elles figurent parmi les organismes à fort potentiel biotechnologique pour des applications biocarburant. Les diatomées sont des organismes symbiotiques issus de la fusion d'un ancêtre hétérotrophe avec une ou plusieurs micro-algues photosynthétiques. Grace à cette histoire évolutive complexe, les diatomées ont un métabolisme très flexible. Comme la plus part des microalgues elles peuvent utiliser la photosynthèse pour leur croissance, mais aussi la mixotrophie, i.e. la capacité de croître en présence de lumière et d’une source de carbone réduit. L'utilisation simultanée de la photosynthèse et de la respiration peut augmenter la productivité de la biomasse des microalgues et réduire ainsi le coût de leur exploitation industrielle. Dans cette thèse j’ai étudié le mécanisme et les conséquences du métabolisme mixotrophique chez la diatomée modèle Phaeodactylum tricornutum. J’ai contribué à étudier le mécanisme moléculaire à la base des interactions énérgétiques entre chloroplaste et mitochondrie. Dans ce travail, nous avons démontré que le NADPH généré dans le chloroplaste est exporté vers la mitochondrie pour générer de l’ATP requis pour la fixation du CO2 dans le chloroplaste. Cette interaction entre les deux organites cellulaires augmente la croissance de diatomées, et suggère que l'utilisation simultanée d’une source de carbone et de l'énergie lumineuse (mixotrophie) devrait augmenter la productivité de la biomasse chez les diatomées. Cette hypothèse a été testée dans la deuxième partie de ma thèse, où j’ai etudié les conséquences de la mixotrophie sur le métabolisme de Phaeodactylum. Grace à une approche métabolomique, transcriptomique, lipidomiques et de physiologie j’ai contribué à éclaircir les principales voies métaboliques (métabolisme centrale, métabolisme des lipides, métabolisme des polymères de réserve) concerné la mixotrophie. Dans la dernière partie de ce travail j’ai optimisé les conditions de culture et la composition du milieu afin d’améliorer la productivité en croissance mixotrophe chez Phaeodactylum. Ce résultat a été validé dans des photobioréacteurs à l'échelle labo pour tester le potentiel de l'exploitation industrielle de cet organisme. / Diatoms are photosynthetic organisms with a strong influence on the global biogeochemistry. Moreover, they are extremely interesting as potential feedstocks for the production of high-value molecules and biofuel. They are endosymbiotic organisms originated by the fusion of a heterotrophic ancestor with one or more photosynthetic microalgae. This has led to an extremely flexible cell metabolism. Like other microalgae, diatoms are able to grow in the presence of both light and of a reduced carbon source. The simultaneous use of photosynthesis and respiration can increase biomass productivity and reduce the energy cost of the industrial exploitation of diatoms.In this project, the mechanism and the consequences of mixotrophic metabolism have been studied in the model diatom Phaeodactylum tricornutum. In the first part, I have studied the molecular mechanism governing the interactions between chloroplast and mitochondrion. We have demonstrated that the NADPH generated in the plastid is exported to the mitochondrion to generate additional ATP, which, once back to the plastid, is used for carbon fixation. Overall, this work shows that the interaction between these two organelles increases carbon fixation and growth in diatoms. We hence suggest that the simultaneous use of carbon and light energy sources (i.e. mixotrophy) should enhance biomass productivity in diatoms. This hypothesis has been tested in the second part of my thesis, where I focused on the consequences of mixotrophy on metabolism. By combining metabolomic, transcriptomic, lipidomic and physiology approaches, I have contributed to elucidate the main pathways targeted by mixotrophy (central carbon, lipid and storage carbon metabolism). In the last part of this work, I have worked on improving the culture conditions and medium composition to boost microalgal productivity by mixotrophy. These conditions have been scaled-up in lab scale photobioreactors, revealing the industrial exploitation potential of Phaeodactylum.

Lake biotic responses to natural climate variability, fire disturbances, and human impacts over the Holocene were studied at two proximate sites in southwestern Québec. Sediments from Lac Noir and Lac Brûlé had annually deposited laminations (varves), enabling for the precise dating of continuous time-series and high-resolution analysis of subfossil diatom assemblages. The Lac Noir (45°46’31”N, 75°8’23”W, 176 m a.s.l.) record spanned ~11000 years of the Holocene. Stratigraphic changes in diatom assemblages of the lake could be divided into early, mid-, and late periods, broadly paralleling Milankovitch-scale climate intervals and vegetation changes inferred from regional palynological records. The early Holocene (11.1-8.0 ka) climate was cooler and dry, vegetation in the region was comprised of Picea-dominated woodlands, and the lake diatom flora included primarily benthic taxa. Warming in the mid-Holocene (8.0-3.6 ka) allowed for stabilization of soils and forests in the catchment, stronger thermal stratification in the lake, and resultant increases in oligo-mesotrophic diatom taxa such as Discostella stelligera. During the late Holocene (3.6 ka to present), an increase in the abundance of deciduous trees (e.g. Betula and Alnus) in response to cooling led to nutrient-enrichment and higher overall lake productivity. The record from Lac Brûlé (45°43’09”N, 75°26’32”W, 270 m a.s.l.) encompassed the last ~1200 years of the late Holocene. Generalized additive models (GAM) revealed a tight coupling between diatoms and catchment-mediated processes (e.g. vegetation and disturbances), which were closely aligned with climate variations. During the Medieval Warm Period (800-1300 CE), pollen-based inferences of warmer summer temperatures were associated with high abundances of Cyclotella bodanica var. intermedia and Cyclotella rossii; this signalled oligotrophic lake conditions and prolonged thermal stratification. The onset of the Little Ice Age (1450-1850 CE) marked a cooling in the region, and a decline in Tabellaria flocculosa str. IIIp indicated increased nutrient loading from the catchment area. Situated less than 300m from Lac Brûlé are remnants of the Wallingford-Back Mine, which ran from 1924-1972 CE; activities at the mine resulted in local changes to nutrient availability and primary productivity at this site. In previous studies of both Lac Noir and Lac Brûlé, pollen records had indicated overall similarities in the vegetation histories in response to climate variability during the late Holocene. Diatom assemblages were influenced by individual lake conditions and were thus unique to each site; nevertheless, they were closely linked with local and regional patterns of vegetation composition. A main point of difference in the paleo-records from both lakes was attributed to a local fire in the Lac Brûlé catchment at 1345 CE, which caused an early decline in hemlock (Tsuga). The decrease in hemlock was seen at Lac Noir only centuries later, and diatoms in each lake responded according to vegetation changes within their own respective catchments. This research shows that high-resolution sampling of lake sediments is able to detect diatom responses to both long-term and abrupt changes in the environment. Individual sites show similarly timed responses of other proxy-indicators, such as pollen and cladocera, to climate and land-use changes. However, distinct differences in the aquatic biota of well-dated proximate sites can be used to identify influences of regional climate variations, which are sometimes masked by localized, non-climatic processes.

Typescript. Includes vita and abstract. Bibliography: Includes bibliographical references (leaves 91-99). Description: xi, 99 leaves : ill., maps ; 29 cm.

La Directive Cadre Européenne sur l'eau impose d'évaluer la qualité des cours d'eau au moyen d'indicateurs chimiques et biologiques dont les diatomées font partie. Les indices basés sur la composition taxonomique et l'abondance relative des taxa de diatomées sont robustes. Cependant, de nombreux échantillons doivent être analysés chaque année alors que l'identification de ces micro-algues en microscopie optique est difficile à cause des incertitudes taxonomiques, et nécessite temps et expertise. Ainsi, des améliorations peuvent encore être apportées pour faciliter le suivi en routine de la qualité de l'eau. Les techniques de biologie moléculaire sont des outils efficaces pour identifier les microorganismes et pourraient donc être utilisées pour améliorer l'identification des diatomées. Les objectifs de cette thèse étaient donc de compléter les connaissances sur la taxonomie des diatomées d'eau douce par des méthodes moléculaires et de progresser dans le développement d'un outil moléculaire permettant l'identification des diatomées dans des échantillons naturels, en vue de son utilisation en bioindication. L'étude de la taxonomie de plusieurs groupes de diatomées a été réalisée en combinant des approches morphologiques et des approches moléculaires. Nos travaux ont montré les capacités des séquences ADN pour discriminer les taxa de diatomées et révéler leurs relations phylogénétiques. L'utilisation de séquences ADN a montré que les critères morphologiques utilisés pour identifier les diatomées ne correspondaient pas systématiquement à leurs relations phylogénétiques. L'utilisation de différents marqueurs a permis des discriminations à différents niveaux taxonomiques. Nos résultats ont également révélé l'importance de combiner des approches complémentaires, morphologiques et moléculaires, pour améliorer notre compréhension des relations entre les différents taxa de diatomées et ainsi stabiliser leur taxonomie. Les séquences ADN permettant une discrimination des taxa de diatomées, nous avons testé un outil moléculaire de séquençage haut-débit, le pyroséquençage 454, dans le but d'identifier les taxa composant les communautés de diatomées. Nous avons ainsi assemblé des bases de séquences de référence bénéficiant d'une identification taxonomique. Nous avons également participé au développement d'outils bioinformatiques nécessaires à l'analyse des données de pyroséquençage. Enfin, nous avons pu tester ces outils pour établir des inventaires taxonomiques de diatomées dans des communautés artificielles (mélanges de souches) et dans des communautés environnementales (biofilms d'eau douce). Ces études ont prouvé le potentiel du pyroséquençage 454 pour étudier les communautés de diatomées à des niveaux taxonomiques précis. La comparaison de différents marqueurs nucléiques a révélé que le marqueur rbcL était le marqueur le plus adapté à l'identification des diatomées par pyroséquençage. En effet, en prenant en compte les bases de séquences de référence, la reproductibilité et les biais de la méthode ainsi que le pouvoir résolutif du marqueur, l'utilisation du rbcL a permis la meilleure estimation de la composition en diatomées d'échantillons complexes. Des progrès devront encore être faits avant de pouvoir utiliser les outils moléculaires pour évaluer la qualité de l'eau par les diatomées. Cependant nos différentes études permettront de guider les prochaines analyses de manière à aboutir à un suivi de la qualité de l'eau basé sur des inventaires moléculaires des taxa de diatomées. / The European Water Framework Directive requires assessing the river quality using chemical and biological indicators among which are diatoms. Indices based on taxonomic composition and relative abundance of diatom taxa are robust. However, thousands of diatom samples are analyzed every year while microscopic identification is difficult due to taxonomic uncertainties, and requires time and expertise. Thus, it is still possible to improve the routine monitoring of water quality. The molecular biology techniques are accurate tools to identify microorganisms and could be used to enhance diatom identification. The objectives of this thesis were therefore to improve our knowledge on the freshwater diatom taxonomy by molecular methods and to progress in the development of a molecular tool in order to identify diatoms in natural samples, thus improving bioindication tools. The taxonomic study of several groups of diatoms was achieved by combining morphological and molecular approaches. Our results showed the capacity of DNA sequences to discriminate diatom taxa and revealed their phylogenetic relationships. The use of DNA sequences showed that the morphological criteria used to identify diatoms do not correspond systematically to their phylogenetic relationships. The use of different markers allowed discrimination at different taxonomic levels. Our results also revealed the importance of combining complementary approaches, morphological and molecular, to improve our understanding of the relationships between different diatom taxa and thus stabilize their taxonomy. As DNA sequences allowed discrimination of diatom taxa, we tested a molecular tool of high throughput sequencing, 454 pyrosequencing, in order to identify the diatom composition of communities. We assembled reference libraries of sequences linked to taxonomic identification and we contributed to the development of bioinformatic tools required to analyze data from pyrosequencing. Finally, we tested these tools to establish taxonomic inventories of diatoms in artificial communities (mixtures of strains) and environmental communities (freshwater biofilm samples). The studies showed the potential of 454 pyrosequencing to accurately analyze diatom communities. The comparison of different nucleic markers revealed that the rbcL marker was the most suitable to identify diatoms using pyrosequencing. Indeed, taking into account reference libraries, reproducibility and bias of the method, and the resolving power of marker, the use of rbcL allowed the best estimation of the diatom composition in complex samples. Improvements will be necessary to use molecular tools in order to assess water quality using diatoms. However our studies lead the way for future experiments in order to achieve a monitoring of water quality based on molecular inventories of diatom taxa.

Dissertação(mestrado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2011 / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-12-16T03:06:44Z No. of bitstreams: 1 Priscila da Fonseca Teixeira.pdf: 335923 bytes, checksum: 69841da63959745c00a7a0e8b7859194 (MD5) / Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-12-18T18:10:59Z (GMT) No. of bitstreams: 1 Priscila da Fonseca Teixeira.pdf: 335923 bytes, checksum: 69841da63959745c00a7a0e8b7859194 (MD5) / Made available in DSpace on 2013-12-18T18:10:59Z (GMT). No. of bitstreams: 1 Priscila da Fonseca Teixeira.pdf: 335923 bytes, checksum: 69841da63959745c00a7a0e8b7859194 (MD5) Previous issue date: 2011 / Na aqüicultura, o sistema sem trocas de água é eficiente e sustentável, permite manejar o balanço entre carbono e nitrogênio, e o desenvolvimento de microorganismos que contribuem na boa qualidade da água, alimentação e sobrevivência do organismo alvo do cultivo. No presente estudo, a composição e densidade de fitoplâncton e protozooplâncton em conjunto com variáveis físico-químicas foram avaliados em viveiros de cultivo de camarão Litopenaeus vannamei (Boone) em sistema sem troca de água em dois tratamentos, com e sem a adição de melaço como fertilizante de carbono. As amostras de água foram coletadas por um período de 70 dias (janeiro a abril de 2009) e os tratamentos apresentaram diferença significativa para o teor dos nutrientes fosfato, silicato e clorofila <20 μm. A clorofila foi dominada pela fração <20μm (>80%) nos dois tratamentos e alcançou os maiores valores (~400 μg L-1) no final do experimento. No viveiro com melaço houve um maior crescimento de cianobactérias filamentosas (Pseudoanabaena spp. e Spirulina sp.), de diatomáceas especialmente Pleurosigma sp. e de ciliados, além da presença de Oxyrrhis marina Dujardin e de Anabaena sp.. No viveiro sem melaço os flagelados e dinoflagelados, especialmente Protoperidinium sp. e outros da ordem Peridiniales foram mais freqüentes e abundantes. Em ambos os tratamentos foi observada uma alta densidade de cianobactérias cocóides e de dinoflagelados (Gymnodiniales e Gyrodinium sp.). Apesar de não terem sido encontradas diferenças estatísticas entre os tratamentos, ficaram claras tendências distintas de composição e densidade do fitoplâncton e protozooplâncton entre os viveiros, indicando a influência da adição de melaço. / In aquaculture the zero water exchange system is efficient, sustainable, and allows the management to balance the carbon and nitrogen compounds through the development of microorganisms contributing to good water quality, feeding and survival of the target organism. In this study, the composition and density phytoplankton and protozooplâncton together with physical and chemical variables were evaluated in shrimp ponds (Litopenaeus vannamei Boone) without water exchange in two treatments with and without the addition of molasses as carbon fertilizer. Water samples were collected during 70 days (January- April 2009). The treatments differed significantly in dissolved inorganic phosphate, silicate and chlorophyll <20 μm. Chlorophyll, dominated by the fraction <20 μm (> 80%), reached the highest values (~400 μg L-1) at the end of the experiment in both treatments. In the pond with molasses, the filamentous cyanobacteria (Pseudoanabaena spp., Spirulina sp.), the diatom Pleurosigma sp. and ciliates reached highest density and the dinoflagellate Oxyrrhis marina Dujardin and the cyanobacteria Anabaena sp. were present. In the pond without molasses, flagellates, and dinoflagellates Protoperidinium sp. and other Peridiniales were more frequent and abundant. In both treatments coccoid cyanobacteria and dinoflagellates (Gyrodinium sp. and other Gymnodiniales) were abundant. Although the differences were not statistically significant, the composition and abundance of phytoplankton and protozooplankton differed over time in both treatments, indicating the influence of the molasses addition.

A detailed geochronological and geochemical study has been undertaken on selected sediment cores from four lowland coastal marsh environments in Argyll, Western Scotland. This region of northern Britain has experienced differential crustal uplift and relative sea-level changes throughout the Holocene in response to glacio-isostatic adjustment. The complex interplay between land movements and relative sea-level continues to influence the morphological development of the Scottish coast. The study of lowland inter-tidal sedimentary environments from this region provides an opportunity to investigate the linkages between current estimated crustal movements, regional relative sea-level rise and the evolution of contemporary coastal saltmarshes derived from the record of historical sedimentation. The four sites are located across a ca. 70 km transect extending from the head of Loch Scridain (western Isle of Mull), across the Firth of Lorne to the head of Loch Etive, (mainland Argyll). Vertical activity distributions of the natural radionuclide 21OPb and anthropogenic isotopes (137Cs and 243Am) have been measured and are used to assess the depositional history of marsh sediment accumulation recorded in the four marsh cores. Down-core activity profiles of radionuclides are only reliable as a means of modelling recent marsh evolution provided no early-diagenetic (redox) reactions have compromised the historical depositional record within the marsh sediments. Solid-phase major and trace element down-core geochemical distributions provide a means of assessing the extent to which post-depositional (redox) reactions may have influenced the reliability of the radiometric dating methods. Marsh sediment geochemistry also serves as a useful proxy for identifying compositional variability over the period of marsh development investigated. Dating of the Argyll saltmarsh cores indicates that over the period corresponding to mature marsh conditions rates of sedimentation vary significantly across the study area. At Loch Scridain an average rate of 1.1 mm yr-1 corresponding to an historical period of ca. 130 years is recorded. Comparison with estimated rates of regional sea-level rise suggest an established asymptotic relationship between marsh accretion and coastal forcing, implying historical crustal stability at this site. At sites within the Firth of Lome (Loch Don and Loch Creran) average rates of 2.5 and 3.3 mm yr-1 are recorded for the ca. 70 year period to 1995 with a figure of 2.2 mm yr-1 recorded in the marsh core from the head of Loch Etive. These values are well in excess of estimated relative sea-level rise during the twentieth century suggesting that these marshes may not yet have reached full equilibrium with sea-level. Microfossil analysis of the Loch Etive core helps to identify a more complex depositional history with an underlying trend of marine transgression for the ca. 110 year period of marsh development recorded in these sediments. Over the most recent period of marsh development (ca. 5 years) a significant increase in the rate of marsh sedimentation at all sites is recorded. This signifies the response of these marshes to a very recent increase in the rate of relative sea-level rise across the region. Comparison with available storm frequency data indicates that the evolution of these marsh environments have not been subject to the influence of significant storm activity over the last in the late Twetieth century. The findings suggest that the more clastic sedimentary composition of the Argyll marshes results in these inter-tidal areas being extremely sensitive to changes in coastal forcing (sea-level rise). The implications of recent relative sea-level rise, current vertical crustal movements and future coastal management are discussed.