Animals living in marine sediments (the second largest habitat on earth) play a major role in global biogeochemical cycling. By feeding on organic matter from settled phytoplankton blooms they produce food for higher trophic levels and nutrients that can fuel primary production. In the Baltic Sea, anthropogenic stresses, such as eutrophication and introductions of invasive species, have altered phytoplankton dynamics and benthic communities. This thesis discusses the effects of different types of phytoplankton on the deposit-feeding community and the importance of benthic biodiversity for fate of the phytoplankton bloom-derived organic matter. Deposit-feeders survived and fed on settled cyanobacterial bloom material and in doing so accumulated the cyanobacterial toxin nodularin. Their growth after feeding on cyanobacteria was much slower than on a diet of spring bloom diatoms. The results show that settling blooms of cyanobacteria are used as food without obvious toxic effects, although they do not sustain rapid growth of the fauna. Since all tested species accumulated the cyanotoxin, negative effects higher up in the food web can not be ruled out. Both species composition and richness of deposit-feeding macrofauna influenced how much of the phytoplankton bloom material that was incorporated in fauna or retained in the sediment. The mechanism behind the positive effect of species richness was mainly niche differentiation among functionally different species, resulting in a more efficient utilization of resources at greater biodiversity. This was observed even after addition of an invasive polychaete species. Hence, species loss can be expected to affect benthic productivity negatively. In conclusion, efficiency in organic matter processing depends both on pelagic phytoplankton quality and benthic community composition and species richness. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: In press. Paper 5: Manuscript.</p>

Paleoenvironmental investigations establish important baseline knowledge of the natural variability of lake systems, to better understand human impacts on the landscape, and the effects of climate change on water resources. By combining long-term environmental history with investigations into modern land use patterns and climatological events, a wider perspective can be reached that has practical applications in water governance. This thesis presents a case study of Lake Basotu (4.37°S, 35.07°E), a crater lake in the Hanang district of north-central Tanzania, which acts as an important source of freshwater for local people. A three-meter long sediment core from an interior crater of Lake Basotu was investigated using proxy records (diatoms, magnetic parameters, and carbon content) and radiometric dating (14C and 210Pb). The Lake Basotu record was then compared to other sediment-based reconstructions from East Africa and records of historical famines to better place it into the timeline and understanding of regional climate dynamics. This work was extended into modern times (1973–2015) by examining lake extent variations in the Landsat satellite archive. Shoreline boundaries for dry-season images were delineated and lake extent was calculated using GIS techniques. This remote sensing record was compared to climatological patterns, meteorological records, and the history of land-use changes in the surrounding district. As a whole, the Lake Basotu record indicates that major fluctuations in lake level are not abnormal; however, human influence has likely increased the lake’s sensitivity to climatic fluctuations. The timing of historical famines in East Africa were linked to periods of shallow lake conditions in Basotu, and the duration of the most extreme lake level changes correlate to a reversal in the 14C age-depth model. Recent variations in lake extent are likely connected to a mechanized wheat farming program implemented in the district as a foreign aid project in the early 1960s. To support the work done in Basotu, a preliminary investigation of sediment from the nearby Lake Babati was undertaken. Sediment from the two lakes indicates that their geographical location may be in a transition zone towards dryer conditions to the south during the Little Ice Age in East Africa. The results of this thesis support that Lake Basotu is an important location for understanding the potential impacts of climate change and human activity on water resources in this region. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Manuscript.</p>

Les diatomées constituent le principal groupe du phytoplancton dans les océans, contribuant à près de 20% de la production primaire globale. Dans leur environnement très variable, les diatomées sont particulièrement efficaces dans leur capacité à ajuster leur activité photosynthétique en dissipant sous forme de chaleur l’énergie lumineuse absorbée en excès, par un processus appelé le « Non-Photochemical Quenching of chlorophyll fluorescence », (NPQ). Chez la diatomée modèle, Phaeodactylum tricornutum, il a été montré que LHCX1, une protéine proche des antennes photosynthétiques, est impliquée dans le NPQ. Par des approches intrégrées de génétique, biologie moléculaire, biochimie, imagerie des cinétiques de fluorescence et spectroscopie ultrarapide, j’ai étudié le rôle de la famille des LHCX chez P. tricornutum. J’ai tout d’abord pu corréler une expression différentielle des 4 gènes LHCX de P. tricornutum avec différentes dynamiques de NPQ et activités photosynthétiques, dans différentes conditions de lumiére et nutriments. En localisant les LHCX dans les differents complexes photosynthétiques et les différents sites de dissipation d’énergie, j’ai pu proposer un modèle de régulation dynamique du NPQ impliquant à court terme principalement LHCX1 au niveau des centres réactionnels, et une autre isoforme, possiblement LHCX3, au niveau des antennes lors d’un stress lumineux prolongé. Enfin, par le criblage d’une série de mutants potentiellement dérégulés dans leur contenu en LHCXs, j’ai pu identifier des lignées avec un NPQ altéré qui pourront constituer des nouveaux outils de recherche. Dans l’ensemble ce travail de thèse a permis de mettre en évidence la diversification fonctionnelle et l’importance de la famille des LHCX dans la fine modulation des capacités de collecte de lumière et de photoprotection, expliquant sans doute en partie le succès des diatomées dans leur environnement très fluctuant. / Diatoms dominate phytoplanktonic communities in contemporary oceans, contributing to 20% of global primary productivity. In their extremely variable environment, diatoms are especially efficient in adjusting their photosynthetic activity by dissipating as heat the light energy absorbed in excess, through a process called “Non-Photochemical Quenching of chlorophyll fluorescence”, (NPQ). In the model diatom Phaeodactylum tricornutum, it has been shown that LHCX1, a photosynthetic antenna-related gene, is involved in the NPQ process. Through integrated approaches of genetics, molecular biology, biochemistry, study of the kinetics of chlorophyll fluorescence yields and ultrafast spectroscopy, I studied the role of the LHCX family in the photoprotection activity of P. tricornutum. I first correlated a differential regulation of the 4 P. tricornutum LHCX genes with different dynamics of NPQ and photosynthetic activity, in different light and nutrient conditions. By localizing the LHCXs in fractioned photosynthetic complexes and the different sites of energy dissipation, I was able to propose a model of dynamic regulation of NPQ capacity involving mainly the LHCX1 in the reaction centers, during short-term high light responses. During prolonged high light stress, the quenching occurs mainly in the antennas, potentially mediated by the LHCX3 isoform. Finally, using photosynthetic parameters, I screened a series of transgenic lines putatively deregulated in their LHCX amount, and I identified lines with altered NPQ, which could represent novel investigation tools. Altogether, this work highlighted the functional diversification and the importance of the LHCX protein family in the fine-tuning of light harvesting and photoprotection capacity, possibly contributing to explain diatoms success in their highly fluctuating environment.

Focalisé sur le groupe phytoplanctonique des diatomées, ce travail de thèse a permis d'étudier l'impact du réchauffement climatique et de l'acidification des océans afin d'appréhender la réponse de ce taxon au changement climatique actuel. L'augmentation de la pCO2 atmosphérique depuis la première révolution industrielle est à l'origine de l'augmentation de la concentration en carbone inorganique dissous (DIC) dans l'océan de surface, et donc d'une acidification des océans à laquelle s'ajoute un réchauffement de l'océan de surface conduisant finalement à l'extension des zones oligotrophes très stratifiées et pauvres en sels nutritifs. Différentes approches in situ et au laboratoire ont donc été utilisées lors de ce travail de thèse afin de mieux comprendre la place des diatomées dans une province oligotrophe et d'apprécier ensuite leur réponse à un réchauffement et une acidification dans un «chémostat oligotrophe», limité en phosphate. / Specifically orientated on the diatoms' phytoplanktonic group, this work tryed to understand the impact of warming and ocean acidification on diatoms and aimed at understand the taxon's response to the ongoing climate change. Amospheric pCO2 increase since the first industrial revolution lead to the augmentation of dissoveld inorganic carbon (DIC) concentration in the surface ocean, and thus to the ocean acidification, accompanied by an ocean surface warming leading finally to the extension of oligotrophic areas well stratified and nutrient depleted. Different in situ and lab techniques were used in order to better understand the diatom role in oligotrophic system and their response to warming and acidification in an oligotrophic chemostat, limited by phosphate.

Situé en France dans l’Aveyron, le bassin minier de Viviez a été soumis pendant plus d’un siècle à des rejets métalliques (principalement Cd et Zn) et est à l’origine de la contamination de l’estuaire de la Gironde, mise en évidence dans les années 1970. C’est dans ce contexte de pollution avérée que d’importants travaux de remédiation des sols ont été entrepris dès 2007. Les principaux objectifs de cette thèse résidaient en la caractérisation des premiers impacts de la remédiation sur l’amélioration de l’état chimique et écologique de l’hydrosystème via l’étude des biofilms périphytiques et des bivalves filtreurs Corbicula fluminea. En prévision des effets à plus long terme de la remédiation, il s’agissait en second lieu d’évaluer les capacités de décontamination des deux modèles biologiques et de s’intéresser à la restructuration des communautés diatomiques en réponse à une levée du stress métallique par transplantations in situ ou en laboratoire. Le suivi des bioaccumulations métalliques in situ réalisé entre 2008 et 2010 a révélé la rémanence d’un très fort gradient de contamination, à l’origine d’importants clivages communautaires dans les biofilms diatomiques. De plus, une augmentation de la pression métallique a été mesurée in situ en aval du site industriel en 2010 certainement en relation avec les travaux d’excavation. Des études de décontamination ont été menées en laboratoire après l’exposition des organismes in situ au cours de deux saisons. Chez Corbicula fluminea le Zn a été très rapidement dépuré, tandis que 15 mois n’ont pas suffi à obtenir la décontamination totale du Cd, estimée complète par modélisation après 740 à 1360 jours en fonction des saisons d’exposition. Bien que le potentiel de récupération des biofilms soit apparu rapidement en conditions naturelles après transplantation, les études de laboratoire menées sur plusieurs semaines en canaux n’ont pas abouti à une décontamination complète du Cd après 100 jours, qui a été estimée totale après 150 à 450 jours en fonction des saisons d’exposition. Malgré des prémices de restructuration, aucun retour vers des communautés de type témoin n’a pu être mis en évidence. Ces études ont souligné l’importance des phénomènes de migration d’espèces dans le potentiel de récupération des biofilms. Enfin, une étude portant sur les tératologies de diatomées a révélé leur maintien prolongé dans la population malgré l’arrêt de la contamination. L’ensemble de ces études a mis en évidence la complémentarité de l’utilisation des deux modèles biologiques, capables d’intégrer et de réguler différemment les contaminants, pour évaluer leur potentiel de récupération dans un contexte de gestion corrective de l’hydrosystème. / Located in France, in Aveyron, the mining basin of Viviez was submitted for over a century to metal discharges (mainly Cd and Zn) and was proven in the 1970s to be the source of the contamination of the Gironde estuary. In this context, significant soil remediation works were initiated in 2007. The main objectives of this thesis focused on the characterization of the first impacts of remediation on the chemical and ecological improvement status of the hydrosystem via the study of periphytic biofilms and filter-feeding bivalves Corbicula fluminea. In anticipation of the long-term effects of the remediation, a second part was devoted to evaluate the decontamination capabilities of the two biological models and to focus on the restructuring capacities of diatomcommunities in response to metal stress by translocations in situ or to laboratory. Monitoring of metal bioaccumulation carried out in situ between 2008 and 2010 revealed the persistence of a strong gradient of contamination, causing major shifts in the diatom communities of biofilms. In addition, an increase in metal contamination pressure was measured down streams the industrial site in 2010, certainly in relation with the excavation works. Decontamination studies were conducted in the laboratory after in situ exposure of organisms during two seasons. Corbicula fluminea showed fast depuration of Zn, while 15 months were not long enough to get the total decontamination of Cd, estimated complete after 740 to 1360 days according to the exposure season. Although the potential for metal decontamination of biofilms appeared to be rapid under natural conditions after transplantation, laboratory studies conducted over several weeks in artificial streams did not result in complete decontamination of Cd after 100 days, and was estimated complete after 150 to 450 days according to the exposure season. Despite the beginnings of restructuration, no return to communities similar to controls could be observed. These studies have emphasized the importance of the phenomena of species migration in the recoverypotential of biofilms. Finally, a study focussing on diatom teratologies revealed their long persistence in the population despite the stop of the contamination. All these studies demonstrated the complementary usefulness of both biological models, which differently integrate and regulate contaminants, to assess their recovery potential in a remediation context of the hydrosystem.

Diatoms are unicellular, eukaryotic microalgae inhabiting nearly all aquatic habitats. They are famous for their micro- and nanopatterned silicabased cell walls, which are envisioned for various technologic purposes. Within this review article, we summarize recent in vivo modifications of diatom biosilica with respect to the following questions: (i) Which metals are taken up by diatoms and eventually processed into nanoparticles (NPs)? (ii) Are these NPs toxic for the diatoms and––if so––what factors influence toxicity? (iii) What is the mechanism underlying NP synthesis and subsequent metabolism? (iv) How can the obtained materials be useful for materials science?

Die Schwingungsspektroskopie, besonders die Raman-Spektroskopie, stellt ein wichtiges Werkzeug für Untersuchungen von Biomineralien dar. Raman-Spektroskopie wurde zur Untersuchung der organischen und anorganischen Bestandteile von Schwammskeletten eingesetzt. Die Raman-Spektroskopie trug auch zur Charakterisierung von biomimetischen Silikat-Präzipitaten bei. Durch ortsaufgelöste Raman-Spektroskopie konnte erstmalig die Verteilung von organischem Material in den extrahierten Silikatzellwänden von Kieselalgen nachgewiesen werden. Die ortsaufgelöste Raman-Spektroskopie wurde ebenfalls zur Untersuchung des SERS-Effekts an Zellwänden von Kieselalgen an die Silber-Nanopartikel gekoppelt waren eingesetzt.

The Quaternary Paleoecological Analysis of the Soos National Nature Reserve The aim of this proposed diploma thesis is to describe the structure of diatom communities in the diatomite deposits of the Soos National Nature Reserve and compare the finding of this thesis with those of older publications. Another aim was to reconstruct the history of the basin trough with the outputs of diatom analysis accomplished in the 3,4 m long sediment profile. The similarity of diatom communites in individual diatomite types was also tested. Key words: subfossil diatoms, Soos National Nature Reserve, paleolimnology, Late Glacial, Holocene

The influence of human activity on surrounding environments is an important field of research. With respect to aquatic settings, lacustrine deposits provide excellent proxies of environmental change since the sediment accumulates at a relatively constant rate, recording environmental change. This study employs isotopic, mineral, and chemical records from Farmington Bay freeze cores, in particular δ13C, δ15N, and 210Pb isotopes as well as phosphorus level fluctuation and trace metal analysis. In particular, 210Pb isotopes permit estimation of the age of sediment with depth and δ15N, δ13C, and concentration of P provides a record of changing nutrient sources and level of eutrophication. Results from 210Pb isotopes have allowed ages to be assigned to depths along the core dating back roughly 100 years at 30 cm. At this depth, a dramatic shift in the δ15N isotope is observed. Initial δ15N levels indicated a nutrient source related to agriculture. However, beginning around 100 years ago, the δ15N shows the main nutrient source for the bay became wastewater which correlates to the completion of a sewage canal in 1911 that began routing wastewater directly into the bay. Results have also shown a large rise in phosphorus levels beginning around 1970 which may be due to the construction of the automobile causeway that isolated Farmington Bay from the rest of the Great Salt Lake.

Microalgae are gaining more attention for several reasons such as being potential producers of sustainable fuel, for use as health supplements and in skincare. Simris Alg is a Swedish company that produces Omega 3 supplements from a primary producer of these fatty acids - the algal diatom Phaeodactylum tricornutum, which is a sustainable alternative to Omega 3 derived from fish. Omega 3 fatty acids constitute a small fraction of the total algal biomass, and to increase profitability and utilize all of the biomass, the purpose of this thesis project is to present potential applications for the residual material that is left after oil extraction. A general composition study was made of Simris Alg algal residue material, and results are compared to those found in previous studies of P. tricornutum biomass. An optimization of the fractionation is needed to separate the storage carbohydrate chrysolaminarin and cell wall component glucuronomannan, followed by analysis for confirmation. Also, it would be interesting to separate chitin, if there is any, since despite the presence of chitin synthases, it is unclear whether the diatom actually produces chitin. When gathering information, no actual experimental characterization of carbohydrate active enzymes involved in synthesis of the main carbohydrates investigated were found. Such information would be useful to increase production of the carbohydrate of interest, if valuable applications are found. Potential applications of various cell components, such as carbohydrates, in skincare would be interesting to investigate, as well as optimizing fucoxanthin extraction for use as an additional high value product next to Omega 3.