Diatoms are microscopic, photosynthetic, single-celled organisms that are useful in studies of water qualities (eg pH, nutrients, salinity). By analyzing changes in the species composition of diatoms back in time, gives an opportunity to interpret the marine environment affected by various factors (Andren et al, 1999). The aim of the study was to study changes in diatom abundance and composition in Hallsfjärden, a bay in the Baltic Sea located north of Himmerfjärden in Södertälje. The site was chosen because it is a bay that is assumed to have a large environmental impact due to external factors such as increased population growth, water treatment plants, industrial areas, dredging and a link to Lake Mälaren. The purpose of the study therefore to investigate whether there was an environmental impact in Hallsfjärden, in order to draw conclusions about what happened in the area and what has affected the water the last 100 years.      The survey is conducted by sampling sediment cores, studied by biostratigraphy of fossil diatoms to reconstruct past environmental conditions. The results of the analysis showed that oxygen deficiency was a particular problem, which is related to the eutrophication that are threatening some diatoms and thereby changes the species composition of ecosystems in Hallsfjärden. A plausible interpretation of the analyze results is that Hallsfjärden was adversely affected by the Södertalje area's population growth and Himmerfjärdsverkets startup by high emissions of nutrients. It has on the other hand appeared a positive impact for Himmerfjärdsverkets gradually improved purification with clearer water conditions. Hallsfjärden have proved to be a particularly sensitive ecosystem in this study, with low salinity and strong thermocline, which means that it is more affected by eutrophication and pollution in its drainage area. This causes a problem of eutrophication in Hallsfjärden due to the bay showing the influence of the surrounding areas and its emissions, which later exports further to the Baltic Sea via Himmerfjärden with the southbound flow. / Kiselalger är mikroskopiska, fotosyntetiserande, encelliga organismer som är användbara vid studier om vattenkvalitéer (till exempel pH, näringsämnen, salthalt). Genom att analysera förändringar i artsammansättningen av kiselalger bakåt i tiden kan tolkningar göras om hur havsmiljön påverkats av olika faktorer (Andrén m.fl., 1999). Målet med studien var att studera förändringar i kiselalgernas förekomst i Hallsfjärden, en havsvik i Östersjön belägen norr om Himmerfjärden i Södertälje. Platsen valdes för att det är en havsvik som antas ha stor miljöpåverkan på grund av yttre faktorer såsom en ökad befolkningstillväxt, reningsverk, industriområden, muddring och en kontakt med sjön Mälaren. Syftet med studien var därmed att undersöka om en miljöpåverkan fanns i fjärden, detta för att kunna dra slutsatser om vad som hänt samt vad som påverkat vattenområdet de senaste 100 åren.      Undersökningen är utförd genom provtagning av sedimentkärnor som undersökts avseende biostratigrafin av fossila kiselalger för att rekonstruera tidigare miljöförhållanden. Analysresultatet visade att syrebrist var ett utmärkande problem, vilket i samband med eutrofiering hotar vissa kiselalgsarter och förändrar därmed artsammansättningen i ekosystemen i Hallsfjärden. En sannolik tolkning av analysresultatet är att Hallsfjärden påverkats negativt av Södertäljeområdets befolkningstillväxt och Himmerfjärdsverkets uppstart genom höga utsläpp av näringsämnen. Det har å andra sidan synts en positiv inverkan efter Himmerfjärdsverkets successivt förbättrade rening med klarare vattenförhållanden. Hallsfjärden har i studien visat sig vara ett särskilt känsligt ekosystem med låg salthalt och starka språngskikt, vilket gör att det påverkas mer av eutrofiering och föroreningarna i området. Detta medför en övergödningsproblematik i Hallsfjärden, då fjärden visar en påverkan av omkringliggande områden och dess utsläpp av föroreningar, vilka även sedan exporteras ut i Östersjön via Himmerfjärden med den sydgående strömmen.

Increased groundwater usage, rainfall decline and activities such as mining have resulted in the acidification of certain wetlands in the south-west of Western Australia. This study investigated the influence of pH, the factor most commonly associated with acidification, on the invertebrate and diatom community structure of 20 wetlands in the south-west region of Western Australia. Few studies in Western Australia have investigated both biotic groups, particularly in relation to pH. Consequently, this study examined the comparative sensitivity of the two biotic groups to pH in order to identify the most effective biotic tool for assessing the ecological impacts of pH decrease. The wetlands included in this study displayed a wide range of pH from acidic (pH < 6.5) to alkaline (pH > 7.5). Other environmental parameters were also variable. Separation of the wetlands into three pH groups; Group 1 – acidic, Group 2 – circumneutral and Group 3 – alkaline, demonstrated that the acidic Group 1 wetlands generally had higher electrical conductivity than the remaining groups. This was probably due to the association of many Group 1 sites with mining and acid sulphate soils. Seasonal trends in environmental variables across the three pH groups were mostly unclear although some trends were evident within the individual pH groups. The study showed that invertebrate community structure differed in response to pH. However, the results also demonstrated that invertebrate distribution patterns were influenced by other factors. / Potential indicator species identified from the study included Macrothrix indistincta and Tanytarsus fuscithorax/semibarbitarsus which were abundant in acidic waters and Alona quadrangularis which was common in circumneutral sites. Taxa such as Calamoecia tasmanica subattenuata were common over a wider range of pH (acidic to circumneutral) but may still have potential to act as indicators of pH decline. Diatom community structure was also shown to be influenced by pH, with the variable identified as a major determinant of diatom distribution patterns. Nitzschia paleaeformis and Navicula aff. cari were generally recorded from acidic wetlands and are potentially useful as indicators of low pH conditions. Brachysira brebissonii and Frustulia magaliesmontana were also identified as species with the potential to indicate pH decline. In contrast, taxa including Gomphonema parvulum, Staurosira construens var. venter and Nitzschia palea were generally associated with moderate to high pH levels. A comparative study of the two biotic groups using multivariate analyses revealed that diatoms were more sensitive to pH than invertebrates. Further investigation with a larger number of environmental variables would be necessary to ascertain the other factors primarily influencing invertebrate community structure. Nonetheless, the findings imply that diatoms and invertebrates differ in their responsiveness to various environmental factors and may provide complementary information on the integrity of a system. Multivariate analyses on an expanded data-set of 40 sites found that pH accounted for the greatest amount of variation in the data and was conducive to the development of a diatom-based pH inference model. / The strongest model was produced using weighted averaging (WA) with classical deshrinking. While the model displayed a high correlation coefficient, the prediction error was also relatively high, probably as a result of the comparatively small and heterogeneous data-set. Incorporation of the data into a larger training set would be likely to improve the predictive ability. Applications for the model include pH reconstructions or use in monitoring programs. The current study has shown that pH is an important variable influencing both invertebrate and diatom community structure in wetlands in the south-west of Western Australia. However, the greater sensitivity of diatoms to pH suggests that they would be the most effective tool for the biological monitoring of pH in wetlands threatened or impacted by acidification. An integrated monitoring program including both diatoms and invertebrates may provide additional information on the impacts of pH decline and the overall integrity of the systems and should be investigated further.

This thesis investigates how variations in the oxygen isotopic composition of lake waters in northern Fennoscandia are recorded in lake sediment archives, especially diatoms, and how these variations can be used to infer past changes in climate and atmospheric circulation. Results from analyses of the oxygen isotopic composition of lake water samples (δ18Olakew) collected between 2001 and 2006 show that δ18O of northern Fennoscandian lakes is mainly controlled by the isotopic composition of the precipitation (δ18Op). Changes in local δ18Op depend on variations in ambient air temperature and changes in atmospheric circulation that lead to changes in moisture source, vapour transport efficiency, or winter to summer precipitation distribution. This study demonstrates that the amount of isotopic variation in lake water δ18O is determined by a combination of the original δ18Olakew, the amount and timing of the snowmelt, the amount of seasonally specific precipitation and groundwater, any evaporation effects, and lake water residence time. The fact that the same isotope shifts have been detected in various δ18Olakew proxies, derived from hydrologically different lakes, suggests that these records reflect regional atmospheric circulation changes. The results indicate that diatom biogenic silica isotope (δ18Odiatom) records can provide important information about changes in atmospheric circulation that can help explain temperature and precipitation changes during the Holocene. The reconstructed long-term Holocene decreasing δ18Op trend was likely forced by a shift from strong zonal westerly airflow (relatively high δ18Op) in the early Holocene to a more meridional flow pattern (relatively low δ18Op). The large δ18Olakew depletion recorded in the δ18O records around ca. 500 cal yr BP (AD 1450) may be due to a shift to more intense meridional airflow over northern Fennoscandia resulting in an increasing proportion of winter precipitation from the north or southeast. This climate shift probably marks the onset of the so-called Little Ice Age in this region. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: In press. Paper 2: Submitted. Paper 5: In progress.

Domoic acid (DA), a potent neurotoxin that has the potential to cause amnesic shellfish poisoning (ASP), is produced by members of the marine diatom genus Pseudo-nitzschia. Outbreaks of ASP in humans and of DA poisoning in birds and marine mammals have been reported across the United States and Canada since the late 1980's. Pseudo-nitzschia species can be extremely abundant in Florida waters, with densities often exceeding 106 cells/L, and sometimes exceeding 107 cells/L. Based on preliminary data, it is evident that at least nine species of Pseudo-nitzschia are found in Florida coastal waters. At least six of these species are known to produce DA in other parts of the world, and some are morphologically identical to some of the major toxin-producing species in Californian and Canadian waters. Despite the strong presence of Pseudo-nitzschia, there has never been a report of ASP or a DA-related animal mortality event from Florida. Data collected from 2004 to 2011 show maximum Pseudo-nitzschia abundances exceeded 4 x 107 cells/L. Six species of Pseudo-nitzschia were identified from central west and southwest Florida waters via light and electron microscopy. This is the first report of P. micropora from the Gulf of Mexico. Additionally P. calliantha, P. cuspidata, and P. pungens were identified as producers of DA in Florida coastal waters; although cell quotas of DA were low. Low levels of DA were detected in about one third of the water samples analyzed and DA concentrations measured in the majority of shellfish from the study area were at least an order of magnitude below the regulatory limit of 20 µg/g, suggesting that Pseudo-nitzschia currently poses little threat to human health in Florida. However, DA production in Pseudo-nitzschia species has been shown to be variable and dependent on nutrient conditions, indicating that the potential for DA-related events to occur in Florida warrants further investigation.

Les éléments génétiques transposables (ET) sont des séquences d’ADN capables de se déplacer dans tous lesgénomes sous certaines conditions. Les ET ont des structures et des modes de transposition qui lesdifférencient en plusieurs groupes. Les éléments de la famille mariner sont ubiquistes ; lorsqu’ils sont actifs, ilsproduisent une transposase qui coupe l’élément et l’insère dans un autre locus. Des fragments d’éléments detype mariner (MLE) ont été précédemment identifiés chez la diatomée marine Amphora acutiuscula et ils semblaientactifs en condition de stress thermiques. Les diatomées sont caractérisées par une paroi siliceuse ornementée et,dans le milieu marin, elles jouent un rôle primordial dans les chaînes alimentaires.Dans le présent travail, par des méthodes de biologie moléculaire et de bioinformatique, nous avons recherché et caractérisé des MLE complets, et précisé leur activité en conditions de chocs thermiques et métalliques (cuivre et zinc). L’analyse des séquences amplifiées a mis en évidence la présence de MLE particuliers chez cette diatomée qui code une transposase ayant une triade catalytique DD43D jamais décrite jusqu’à présent.L’analyse phylogénétique place les MLE de diatomées dans une sousfamille différente mais proche de celle desMLE de plantes. Parmi les nombreuses copies de MLEprésentes dans le génome d’A. acutiuscula, certaines sont exprimées lorsque la diatomée est placée pendant 2 à 5 heures à unetempérature inférieure à sa température de culture. Par contre, l’expression des MLE n’a pas été mise en évidence chez cette espèce soumise aux stress métalliques appliqués. / Transposable elements (TE) are DNA sequences able to move in all genomes depending on conditions. TE have different structures and transposition mechanisms. Tc1-mariner elements are ubiquist ; when they are active, they produce a transposase which cuts and inserts the element into another locus. Fragments of mariner-like elements (MLE) hadpreviously been identified in the marine diatom Amphora acutiuscula and they seemed active under thermal stress. Diatoms are characterized by a siliceous ornamented cell wall and, in the ocean, they play a major role in trophic networks.In this work, with biomolecular and bioinformatic methods, we have searched for and characterized full length MLE, and precised their activity under thermal and metal (copper and zinc) stresses. The analyse of the DNA sequences obtained highlighted that MLE in diatoms are particular and that they encode a transposase which has a DD43D catalytic triad neverso far depicted. The phylogenetic analyse arranged diatom MLE in a subfamily different and close to that of plant MLE. Among the numerous MLE copies present in the genome of A.acutiuscula, some were expressed when the microalga was put at a lower temperature than the culture temperature for 2 to 5 hours. Conversely, metal stresses we applied did notinduce MLE expression in this species.

The subject of this thesis is selected parameters cement mortars with partial replacement of Portland cement diatomaceous earth. This work provides information on the basic properties of diatomaceous earth and its deposits with a focus on deposit in Borovany. From the properties is very important pozzolanic activity due to the high content of amorphous silica of this soil. The main use of diatomaceous earth is in the area filtration and is used widely as a nutritional supplement. In the building industry, diatomite can be applied as an admixture to mortar and concrete, where it can, with its abilities, improve some physical mechanical properties. In the experimental part was diatomaceous earth, in its raw and calcined form, tested as admixture for cement pastes and mortars. The main criterion for evaluating these composites was bulk density, flexural and compressive strength. It was also investigated mineralogical composition, microstructure, freeze–thaw resistance and sulfate resistance.

The silica-based cell walls of diatoms are outstanding examples of nature’s capability to synthesize complex porous structures with genetically controlled patterns from the nanometer scale to the range of hundreds of micrometers. Formation of the cell wall building blocks (valves and girdle bands) occurs in membrane-bound compartments, termed silica deposition vesicles (SDVs), which are unique organelles in silica-forming protists. Isolation of the SDVs has not yet been achieved, which has severely hampered the efforts to understand the mechanisms of biological silica morphogenesis. The present thesis aimed to address this shortcoming. The foundation was the development of an improved cell cycle synchronization and a fluorescence labeling method for the model diatom Thalassiosira pseudonana that enabled rapid identification of valve SDVs in a cell lysate. Correlative fluorescence and electron microscopy allowed visualizing the development of valve silica with unprecedented spatio-temporal resolution. Elemental analysis and demineralization of immature valves provided the first direct chemical evidence that silica morphogenesis is an interplay of inorganic and organic molecules inside the valve SDVs. Cryo TEM imaging of valve SDVs indicated the formation of organic patterns that precede silica depostion. From these observations, an organic biomolecule dependent, liquid-liquid phase separation based model for pore formation in the diatom T. pseudonana was proposed. The second part of this thesis was focused on the enrichment of valve SDVs from T. pseudonana and the subsequent proteomics based identification of more than 40 potential valve SDV proteins. Among these, three diatom-specific proteins contained conserved protein protein interaction domains (ankyrin-repeats) and were surprisingly predicted to be located in the cytoplasm. The fluorescent tagging of the three proteins (termed dANK1-3) confirmed their association with the valve SDVs. When the respective dank genes were knocked out by CRISPR/Cas9, the valves displayed permanent anomalies in the quantity and the pattern of ~22 nm sized pores. Double knockout mutants lacking both dank1 and dank3 were almost completely devoid of pores. The analysis of valve morphogenesis in the single and double knockout mutants revealed phenotypic changes that were consistent with the liquid-liquid phase separation based model for pore pattern formation in diatom biosilica. The work of this thesis has provided for the first time direct access to valve SDVs, which has opened entirely new possibilities for studying the composition, properties, and working mechanism of an organelle that forms a complex shaped mineral.

Detta projekt fokuserar på att undersöka dynamiken hos partiklar inom en-partikelsystem samt sammankopplade partiklar i tvåpartikelsystem genom tillämpning av numeriska metoder. Tvåpartikelsystemet som studeras är NaI-molekylen och dess dynamik, där beteendet undersöks efter systemet utsatts för en femtosekundslaserpuls. För att uppnå projektets mål utformas numeriska metoder med hjälp av finita differenser och Arnoldis tidsintegrationsalgoritm samt Runge-Kutta 4. Metoderna utvärderas med hjälp av den kvantharmoniska oscillatorn som har en analytisk lösning. Konvergensen för de olika ordningarnas finita differenser testas på den tidsoberoende Schrödingerekvationen för systemet. Arnoldi och RK 4 utvärderas på den tidsberoende Schrödingerekvationen. Baserat på dessa resultat görs en tidkonvergens- och tidseffektivitetsanalys för tidsstegningssmetoderna. Studien visar på att Arnoldi-metoden uppvisar ett större stabilitetsområde, vidare visas det att RK4 är den mindre beräkningstunga metoden för den kvantharmoniska oscillatorn. Resultatet av förstudien visar att finita differenser av åttonde ordningen ger den mest noggranna numeriska approximationen, utöver det görs avvägningen att tidsstegningsmetoderna kräver ytterligare undersökning. Därefter tillämpas den numeriska metoden för att analysera dynamiken hos NaI-molekylen. Tidseffektivitetsstudien för denna del av projektet visar att Arnoldi med 10 iterationer är mest passande för resten av projektet på grund av dess stabilitetsområde samt fördelaktiga hantering av större mer komplexa Hamiltonianer. Simuleringarna av tvåpartikelsystemet visar att när laserns våglängd varierar, varierar den energimängd som tillförs till systemet. Detta kan ses i att populationsnivån på den övre potentialytan är högre för kortare våglängder, och även i att perioden för oscillationerna är längre. När varaktigheten hos laserpulsen ökas observeras en större population på den högre energinivån. Detta eftersom en lång pulslängd leder till en minskad variation i population av energinivåerna på de exciterade vågfunktionerna. För laserpulser vars våglängd korresponderar med rätt energi för excitation leder det till en högre population av exciterade vågfunktioner. Projektets resultat bidrar till en djupare grundläggande förståelse av hur olika parametrar hos femtosekundslasrar påverkar kemiska reaktioner och dynamik på submolekylär nivå.

Paleoclimatic archives, such as lake sediments, extend our understanding of terrestrial and aquatic ecosystem dynamics in relation to climate variability beyond the period covered by instrumental data. In this context, annually laminated (i.e. varved) lake sediments are particularly valuable, as they offer high temporal resolution and undisturbed sediment. However, in order to extract reliable climate information from lake sediments, a careful calibration with the processes controlling the sediment formation is essential. This thesis combines limnological and paleolimnological data from a varved, boreal lake in northern Sweden (Nylandssjön, Nordingrå) collected over different time scales. The main aim of the thesis is to gain a more refined insight into which processes are reflected in the sedimentary diatom assemblage. More specifically, sequential sediment trap records were coupled with physical, chemical and biological lake monitoring and environmental data for comparison and validation with the varved sediment record. The main result of the thesis is that timing, succession and inter-annual variability of key limnological and environmental processes (e.g. ice-cover duration, lake over-turn or catchment run-off) are of major importance for the sedimentary diatom assemblage formation. Continuous monitoring of physico-chemical parameters over three consecutive years identified varying winter air temperature as a major factor influencing in-lake processes and hence the diatom record. Timing of lake over-turn and catchment run-off seemed to be the driver for monospecific diatom blooms, which are reflected in the annual sediment signal. The integrated annual diatom signal in the sediment was dominated by spring or autumn blooms, resulting either from a Cyclotella glomerata dominated spring bloom after relatively warm winter conditions, or a Asterionella formosa dominated autumn bloom after relatively cold winter conditions. The analysis of the diatom stratigraphy in the varved sediment over several decades corroborated the importance of climatic variables (late winter air temperature and NAO), even though the variables with the most predictive power for variance in the diatom data were associated with sediment composition (C, N and sedimentation rate) and pollution (Pb and Cu). Overall, the analysis of the drivers of inter-annual and decadal diatom assemblage fluctuations emphasizes the importance of winter air temperature, indicating that weather extremes may be disproportionately represented in annual sediment records in contrast to nutrient concentrations or sedimentation rate.

Orientador: Denise de Campos Bicudo / Resumo: Este estudo baseou-se em um banco de dados limnológicos e biológicos (diatomáceas de sedimento superficial e da coluna da água) de 33 reservatórios com gradiente trófico (ultraoligotrófico a hipereutrófico) distribuídos na região sudeste do Estado de São Paulo. Visou, como primeira etapa, calcular os ótimos e as tolerâncias ecológicas (etapa de regressão) das espécies de diatomáceas com a finalidade de propor um índice de diatomáceas para avaliar o estado trófico de represas, bem como um modelo de função de transferência diatomácea-fósforo (etapa de calibração) para inferir níveis pretéritos de fósforo da água. Além disso, visou avaliar o efeito da eutrofização sobre a homogeneização taxonômica e funcional das comunidades de diatomáceas. As amostras do sedimento superficial (n = 113) e do plâncton (verão e inverno, n = 226) foram obtidas entre 2009 e 2014. O método da média ponderada (WA) foi utilizado para a etapa de regressão (ótimo e tolerância das espécies), e modelos de regressão clássica e inversa foram testados para a etapa de calibração para a proposição do índice trófico de diatomáceas e para o modelo de função de transferência diatomácea-fósforo. Foram calculados os ótimos e as tolerâncias de fósforo total para 58 (sedimento superficial) e 53 (plâncton) espécies de diatomáceas. O modelo proposto com base nas diatomáceas do sedimento superficial apresentou melhor habilidade (r2 0.71, p<0.001, RMSE 49.43 μg L-1) do que as planctônicas para proposição do índice de esta... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This study was based on a limnological and biological database (surface sediment and water column diatoms) of 33 reservoirs with trophic gradient (ultraoligo- to hyperereutrophic) distributed in the southeastern region of São Paulo State. The first aim was to calculate the optimum and ecological tolerances (regression stage) of diatom species in order to propose a diatom index to evaluate the trophic state of reservoirs, as well as a model of diatom-phosphorus transfer function (calibration step) to infer past levels of water phosphorus. In addition, it aimed to evaluate the effect of eutrophication on the taxonomic and functional homogenization of diatom communities. Surface sediment (n = 113) and plankton (summer and winter, n = 226) samples were obtained between 2009 and 2014. The weighted average (WA) method was used for the regression step (optimal and species tolerance), and classical and inverse regression models were tested for the calibration step for the proposition of the trophic index of diatoms and for the diatom-phosphorus transfer function model. Optimum and tolerances for total phosphorus were calculated for 58 (surface sediment) and 53 (plankton) diatom species. The model based on the surface sediment diatoms presented better ability (r2 0.71, p<0.001, RMSE 49.43 μg L-1) than phytoplankton diatom to propose the trophic diatom index of reservoirs (TDIR). The transfer function model showed high predictive ability (r2 0.80) and was based on 63 diatom species (su... (Complete abstract click electronic access below) / Doutor