Three streams with watersheds of different land uses (urban, agricultural, and forested) were chosen for this study. A composite sample of diatoms was obtained from small rocks in a riffle of each stream and identified to genera. Water chemistry measurements included chloride, sulfate, nitrate, conductivity, pH, alkalinity and temperature.Conductivity, chloride, and sulfate were significantly higher in the urban watershed and lowest in the forested watershed. However, the forested watershed had the highest levels of nitrate, which may have come from groundwater or organic matter decomposition. Alkalinity, pH andtemperature did not vary among watersheds.Diatom diversity was significantly higher in the forested watershed. Several diatom genera, Amphora, Cymbella and Gyrosigma, were positively correlated with nitrate and negatively correlated with conductivity, chloride and sulfate, which indicate their potential use as indicators of water quality. / Department of Natural Resources and Environmental Management

Le microphytobenthos (MPB) des latitudes tempérées est dominé par les diatomées. Deux grands groupes se distinguent, les épipéliques (mobiles) des sédiments vaseux, et les épipsammiques (fixées) des sédiments sablo-vaseux. Afin de mieux comprendre la production des vasières, le MPB a été étudié par des approches du niveau physiologique au niveau écologique. Dans un premier temps, l’étude s’est focalisée sur des expérimentations en laboratoire. La réponse des différents groupes à la lumière a montré que la forme de vie et la mobilité sont en lien étroit avec la capacité de photoprotection physiologique. Ainsi, les diatomées non-mobiles présentent une meilleure photoprotection physiologique que les diatomées mobiles qui peuvent fuir les excès de lumière. Dans une deuxième partie, le travail s’est effectué sur des échantillons ramenés en laboratoire. Des profils de migrations ont été réalisés par mesure continue de la fluorescence. Il a été établi que le MPB présente un rythme de migration interne pouvant être modulé par la lumière. De plus la qualité de la lumière modifie les profils de migration. Il est communément admis que les phases de division cellulaire se dérouleraient en profondeur. La cytométrie en flux permet de vérifier cette hypothèse. Finalement les mesures effectuées en laboratoire ont été comparées à des mesures effectuées directement sur le terrain à l’échelle de la communauté. Il a ainsi pu être vérifié que la photoprotection sous lumière fluctuante est fonction de la population. Pour les populations épipéliques, la photoprotection physiologique ne varie pas au cours des fluctuations lumineuses, laissant supposer que la migration module ces fluctuations. Les populations épipsammiques, quant à elles, modifient leur réponse physiologique en fonction des fluctuations lumineuses. / Microphytobentos (MPB) from temperate latitude is mainly composed of diatoms. Those microorganisms can be separated in two groups: the epipelic one from muddy sediments (composed of mobile diatoms) and the epipsammic one from sandy-muddy sediments (composed of diatoms living attached to their substrate). In order to investigate mudflats’ primary production, the MPB compartment was studied through diverse approaches from the physiological level to the ecological one. In the first place, laboratory experiments (in vitro experiments), focusing on light reaction of epipelic and epipsammic diatoms, showed that their life form and their mobility were strongly connected to their physiological photoprotection ability. Thereby, the motionless diatoms were characterized by higher physiological photoprotection abilities than the mobile ones, which could avoid excess of light. In the second place, the fluorescence of collected samples (in vivo experiments) was measured to acquire diatoms’ migration profiles. The results pointed out an internal and light-regulated migration pattern of the MPB and furthermore highlighted the effect of light quality on migration profiles. Besides, the commonly accepted hypothesis of deep cell division phases was tested and confirmed through flow cytometry experiments. Eventually, laboratory measurements were compared to in situ ones realized at the scale of the whole community. These comparisons revealed that diatoms photoprotection in fluctuating light depended on the targeted populations. Epipelic organisms were indeed characterized by an unvarying photoprotection, diatoms migration regulating alone the effect of light fluctuations. On the contrary, motionless epipsammic populations required a light-regulated photoprotection.

This thesis presents the results of contemporary limnological and palaeolimnological investigations of a series of crater lakes in order to reconstruct the palaeoenvironmental history of western Uganda, East Africa. The research examines questions of spatial and temporal heterogeneity of climate changes in the context of growing human impacts on the landscape over the last millennium. Sediment records from two lakes, Nyamogusingiri and Kyasanduka within the Queen Elizabeth National Park (QENP) were investigated to look at the long term records of climate and environmental change (spanning the last c. 1000 years). Five shorter cores across a land-use gradient were retrieved to assess the impact of human activity on the palaeoenvironmental record over the last ~150 years. High-resolution (sub-decadal), multiproxy analyses of lake sediment cores based on diatoms, bulk geochemistry (C/N and δ13C) and sedimentary variables (loss-on-ignition, magnetic properties and physical properties) provide independent lines of evidence that allow the reconstruction of past climate and environmental changes. This multiproxy approach provides a powerful means to reconstruct past environments, whilst the multi-lake approach assists in the identification and separation of local (e.g. catchment-scale modifications and groundwater influences) and regional effects (e.g. climatic changes). The results of a modern limnological survey of 24 lakes were used in conjunction with diatom surface sediment samples (and corresponding water chemistry) from 64 lakes across a natural conductivity gradient in western Uganda (reflecting a regional climatic gradient of effective moisture) to explore factors controlling diatom distribution. The relationships between water chemistry and diatom distributions were explored using canonical correspondence analysis (CCA) and partial CCA. Variance partitioning indicated that conductivity accounted for a significant and independent portion of this variation. A transfer function was developed for conductivity (r2jack = 0.74). Prediction errors, estimated using jack-knifing, are low for the conductivity model (0.256 log units). The final model was applied to the core sediment data.This study highlights the potential for diatom-based quantitative palaeoenvironmental reconstructions from the crater lakes in western Uganda. Sedimentary archives from the Ugandan crater lakes can provide high-resolution, annual to sub-decadal records of environmental change. Whilst all of the lakes studied here demonstrate an individualistic response to external (e.g. climatic) drivers, the broad patterns observed in Uganda and across East Africa suggest that the crater lakes are indeed sensitive to climatic perturbations such as a dry Mediaeval Warm Period (MWP; AD 1000-1200) and a relatively drier climate during the main phase of the Little Ice Age (LIA; c. AD 1500-1800); though lake levels in western Uganda do fluctuate, with a high stand c. AD 1575-1600). The general trends support the hypothesis of an east to west (wet to dry) gradient across East Africa during the LIA, however, the relationship breaks down and is more complex towards the end of the LIA (c. AD 1700-1750) when the inferred changes in lake levels at Nyamogusingiri and Kyasanduka are synchronous with changes observed at Lakes Naivasha (Kenya) and Victoria and diverge from local lake level records (from Edward, Kasenda and Wandakara). Significant changes in the lake ecosystems have occurred over the last 50-75 years, with major shifts in diatom assemblages to benthic-dominated systems and an inferred increase in nutrient levels. These changes are coincident with large sediment influx to the lakes, perhaps as a result of increasing human activity within many of the lake catchments.

In this study a multiproxy approach (including sedimentary techniques, diatoms, molluscs, foraminifera, sedimentary pigments, isotopes, pollen and plant macrofossils) has been adopted to assess environmental change over the last ~9,000 years at three Danish coastal sites (Kilen, Norsminde Fjord and Korup Sø). Particular focus has been placed on periods of intense human coastal occupation, identifiable in Denmark's rich coastal archaeological record (i.e. shell midden accumulation periods), to test critically, hypotheses that changes in the marine environment were contemporary with major cultural and societal changes over the last ~9,000 years. For example, it has been proposed that a decrease in salinity was responsible for the widespread oyster decline, apparent in the Neolithic layers of a number of Danish shell middens. This hypothesis, however, remains speculative to date, lacking any high-resolution and quantitative salinity data covering the Mesolithic-Neolithic transition. Inside the agricultural era, two more phases of shell midden accumulation occur (i.e. during the Pitted Ware/Single Grave cultural period and the Iron Age), suggesting that people must have returned to the sea at these times for increased exploitation of its resources. A diatom-based salinity transfer function (WAPLS-C3 model, r2 boot = 0.923, RMSEP= 0.36 square root salinity units) based on a trans-Baltic training set has been applied to fossil diatom datasets from each site for quantitative assessment of salinity change over the study period. The multiproxy results presented in this study demonstrate a close connection between environmental change and human exploitation of marine resources over the Holocene. This relationship, however, is complex, with the individual fjord systems often exhibiting spatially different responses (i.e. variations in the sedimentary regime, salinity, productivity and nutrient status) to changes in key forcing mechanisms such as sea level change, climate change and human impact upon the catchment (following the introduction of agriculture). Environmental hypotheses for cultural change are reviewed on the basis of the evidence presented in this study. Diatomenvironmental relationships have also been modelled (using multivariate techniques) at Korup Sø and Norsminde Fjord using proxy data as ‘predictor' variables for changes in the terrestrial and marine environment. These results suggest that a variety of marine, climatic, human and catchment related processes are important in explaining a proportion of the variation in the fossil diatom datasets, but these influences tend to vary temporally throughout the profile (e.g. human impact becomes important after ~3,900 BC).

This thesis uses palaeolimnological records to reconstruct Holocene ontogeny trends from four lakes in south western Greenland. The research addresses four hypotheses investigating how Holocene lake ontogeny trends vary under different climatic settings, how long-term changes in ontogeny relate to periods of established climatic change in the region, the similarities between proxies within the lakes and between the lakes, and the role of vegetation in lake ontogeny. The study region occupies the widest ice-free area of south western Greenland and is characterised by a climatic gradient. The area inland and nearer to the ice-margin is arid, receives less precipitation and is warmer relative to the coastal areas. A paired lake approach, using lake records from two inland lakes and two coastal lakes, was adopted to examine the role of climatic setting upon lake development trajectories. Specifically, diatoms were used to reconstruct DI-alkalinity from the lakes using a DI-alkalinity model created from existing training sets in the region (WA Cla model, r2boot = 0.76, RMSEP = 0.28 log alkalinity units), sedimentary pigments to investigate trends in production and sedimentary parameters to reconstruct organic and minerogenic accumulation rates. All four lakes experienced comparable Holocene long-term ontogeny trajectories; maximum alkalinity in the first ~ 1000 cal. year BP of deglaciation followed by maximum production during the peak of Holocene Thermal Maximum (HTM) warming (~7000 -6000 cal. years BP). Following the HTM, all lakes demonstrated oligotrophication and a decline in pH. Vegetation development and catchment stabilisation at the end of the HTM may be important in determining the onset of oligotrophication in vegetated catchments. However, the impact of vegetation development on lake ontogeny cannot be isolated from the changes in the lakes associated with the colder and wetter climate which occurred at the end of the peak HTM warming. The timings of the large transitions in the ontogeny trajectories are comparable with established periods of Holocene climatic variability in the region; climate forcing drives ontogeny in these lakes. However, there are short-term differences between the lakes indicating that lakes have different thresholds of ecological change and may respond differently to the same climate forcing. It is concluded that ontogeny is driven by climate but lakes may respond differently to forcing depending on catchment specific characteristics which can filter out the climate signal or cause climate to influence the lake in a more direct way.

This thesis presents a study into structural colours that exist in natural samples, the principle aim of which is to produce experimental methods by which these colours may be examined and evaluated. In order to achieve this, previously observed structures are described, electromagnetic theory is summarised and a series of samples are examined constituting examples of the structures present in nature. The first sample discussed is the multilayer in the epicuticle of the buprestid beetle, C. raja. In order to evaluate the refractive indices of the layers contained within this structure, existing optical techniques are used to establish absolute reflection spectra for a number of angles of incidence in both linear polarisations. The approximate design for the structure is obtained by electron microscopy and modelled using Fresnel's equations. This model is then refined by a recursive least squares fitting routine to obtain the refractive indices. The second sample is the diffuse white scattering structure in the scales of two white beetles, Lepidiota stigma and Cyphochilus spp. The reflection from these scales is measured and found to be brilliantly white due to the irregular internal structure of the scales. Comparison of the Fast Fourier Transforms of TEM images of the internal structure with the diffraction pattern obtained from monochromatic laser light diffracting through a single scale demonstrate a link between this structure and photonic effects. The third sample type are found in the scales of the large true weevils, Eupholus schoenherri pettiti and E. magnificus. These scales are shown to have a domained structure in which the domains were oriented differently to each other. Single domains are shown to exhibit different colours at different orientation. The final sample is the highly regular 2-dimensional diffraction grating observed in a marine diatom, Coscinodiscus wailesii. Diffraction is demonstrated by measuring the in-plane diffraction from a single frustule for both monochromatic laser light and white light, showing an enhanced transmission for red wavelengths. Subsequent imaging of the transmitted diffraction pattern allows for the calculation of the transmitted power in each diffracted order.

Les éléments transposables (ET) sont des séquences d‟ADN capables de se déplacer dans les génomes qui les hébergent. Les ET de type mariner (mariner-like element : MLE) ont été caractérisés chez les animaux et chez les plantes à fleurs terrestres mais pas chez les microalgues marines. Dans le présent travail, les MLE ont été recherchés chez les diatomées marines (Bacillariophycées) qui sont des microalgues possédant une enveloppe externe siliceuse. Elles ont colonisé tous les milieux aquatiques et constituent une part majeure du phytoplancton; de ce fait, elles jouent un rôle écologique clé dans le milieu marin.La caractérisation des MLE des diatomées a été réalisée au moyen d‟approches moléculaire et bio-informatique. La présence de MLE dans le génome de 10 espèces de diatomées a été mise en évidence grâce à l‟amplification de fragments d‟environ 380 pb. Ces fragments correspondent à une partie de la séquence conservée codant l‟enzyme responsable de la transposition des MLE : la transposase. L‟analyse des séquences obtenues, par des méthodes phylogénétiques, ainsi que la classification des MLE de diatomées mettent en évidence leur appartenance au groupe des MLE végétaux de la superfamille Tc1-mariner. Néanmoins, les séquences MLE de diatomées divergent considérablement par rapport aux MLE des plantes terrestres. Afin de déterminer si les diatomées ont la capacité de produire la transposase, l‟expression des MLE a été recherchée chez des diatomées soumises à des stress thermiques de courte durée (5 h). Nos travaux montrent que les MLE sont exprimés chez les trois espèces testées incluant la diatomée modèle Phaeodactylum tricornutum dont le génome a été séquencé récemment. L‟expression des MLE des diatomées est variable selon les conditions thermiques et selon les espèces.L‟ensemble de nos résultats suggère que les MLE sont ubiquistes dans les génomes de diatomées et qu‟ils sont présents de manière ancestrale dans la lignée végétale. Les MLE des diatomées forment trois nouvelles sousfamilles de la superfamille Tc1-mariner, la plus répandue des superfamilles d‟ET. De plus, leur expression suggère qu‟il existe des MLE capables de se déplacer dans le génome des diatomées. Si la transposition était vérifiée, ils pourraient alors être développés comme outils de mutagenèse. / Transposable elements (TE) are sequences able to move between two loci in the host genomes. Mariner-like element (MLE) are well characterized in animal and land plant genomes but not in marine microalgae. In this work, we have looked for MLE in marine diatoms (Bacillariophyceae) that are microalgae having a siliceous wall. They have colonized all aquatic environments and are a major component of the phytoplankton, so they play a major role in the ecology of marine environments.To characterize the diatom MLE, molecular and bio-informatics approaches were used. The presence of MLE was detected in ten diatom species which exhibited sequence fragments of about 380 pb. These fragments were identified as a section of the conserved sequence which encodes the enzyme responsible for MLE transposition, the transposase. Phylogeny and classification analysis of these fragments revealed that diatom MLE belong to the Tc1-mariner superfamily, and more precisely to the vegetal MLE group. Nevertheless, diatom MLE sequences diverged from the flowering plant MLE. In order to determine if MLE transposase is produced in diatoms, MLE expression was looked for in diatoms under thermal stresses. Our results showed that diatom MLE were expressed in the three species tested, including the model diatom Phaeodactylum tricornutum which was completely sequenced recently. Diatom MLE expression was dependent on the thermal conditions and on the species.Our results suggest that MLE are widespread in diatom genomes and that they have an ancestral presence in the green lineage. Diatom MLE cluster in three subfamilies in the huge ET Tc1-mariner superfamilly. Finally, the diatom MLE expression detected could reflect the existence of active MLE in diatom genomes. If this hypothesis were verified, it could lead to the development of mutagenesis tools.

iv ABSTRACT Benthic diatoms are due to a number of positive characteristics (such as high abundances, diversified communities, sensitive responses to environmental conditions, capturing long-term changes in the environmental conditions) currently the most commonly used bioindicators of the ecological status of freshwater ecosystems. However, due to problems associated with the use of traditional methods based on species composition (time-consuming identification, presence of species complexes, and requirements for calibration of water quality indexes for geographical regions) searching for alternative methods has been induced. The monitoring of the size structure of diverse diatom communities has been proposed as one of the methods. This approach would mainly eliminate the necessity of time-consuming determination of species. The main purpose of this thesis was therefore to determine the relationship between the size structure of benthic diatom communities, expressed as the relative biovolume, and selected environmental factors (pH, conductivity, habitat type) within freshwater lentic habitats. Furthermore, the variability of biovolume in dependence on environmental variables was compared with the change in species composition. If there would be a similar response pattern of both the biovolume and species...

A traditional species concept of diatoms is based on morphological characters of their siliceous boxes. A multidisciplinary approach to defining species of diatoms has revealed the hidden diversity within the traditionally defined species. But the newly recognized species are morphological variable and indistinguishable by the naked eye. Recent studies showed that different morphotypes show different ecological preferences. This master thesis focuses on the morphology of natural populations of the diatom species complex Frustulia rhomboides which contains both the traditional and the cryptic species, and it engages how the morphology reflects the effects of environmental conditions. Landmark methods of geometric morphometrics were used in order to analyze the morphological variability of diatom frustules of this species complex within various peat bog habitats in the Czech Republic. Selected environmental parameters were measured and the species composition of diatom communities present in the samples was investigated. These data were used to analyze the relationship between the environmental conditions and the cell shape variability within the complex. The analysis revealed the main trends of morphological variability related to different environmental conditions. Two morphotypes characteristic...

La diatomée Haslea ostrearia a longtemps été considérée comme le seul organisme apte à produire un pigment surnuméraire bleu nommé marennine, connu pour son rôle dans le verdissement des branchies des huîtres affinées dans les bassins ostréicoles. Certains des mécanismes et facteurs influençant l’entrée de cette diatomée en phase de reproduction sexuée (auxosporulation) ont été mis en évidence, tels la concentration cellulaire, la qualité de l’éclairement incident, ou le préconditionnement des algues. La découverte dans le cadre d’un projet européen, de populations de diatomées apparentées à H. ostrearia en divers points du globe a conduit à la description et l’identification de trois nouvelles espèces de diatomées bleues : Haslea silbo sp. nov. des îles Canaries, Haslea karadagensis sp. nov., provenant de Mer Noire et Haslea provencialis sp. nov. de Méditerranée Occidentale. La première phylogénie moléculaire de ces espèces de diatomées bleues, ainsi que d’autres espèces de diatomées appartenant au genre Haslea, a été réalisée en utilisant trois marqueurs génétiques, la cassette ribosomale ITS1-5,8S-ITS2, le gène chloroplastique rbcL ainsi qu’un fragment du gène mitochondrial cox1. Ces trois marqueurs moléculaires montrent que les diatomées bleues forment un clade distinct au sein du genre Haslea. De plus, l’existence de deux populations d’H. ostrearia originaires des côtes françaises et suédoises sexuellement compatibles a permis d’étudier la variabilité génétique intraspécifique, en mettant en évidence quelques différences au niveau de la séquence du gène cox1. Ces différences ont également permis d’étudier chez la progéniture obtenue par croisements de ces populations, la répartition et l’héritabilité de l’ADN mitochondrial. Par ailleurs, la spectophotométrie UV-visible et la spectométrie Raman ont été utilisées pour poursuivre la caractérisation physico-chimique des pigments bleus de ces diatomées. L’existence de pigments distincts chez les nouvelles espèces de diatomées bleues a permis de proposer une première classification chimiotaxonomique. Enfin, les activités biologiques de la marennine et du pigment de l’espèce ukrainienne, H. karadagensis, ont été étudiées grâce à la détermination de leurs propriétés antibactériennes et antivirales. / The diatom Haslea ostrearia has long been considered as the only organism able to produce a blue pigment called marennine, known for greening oysters’ gills in fattening ponds. Key factors for the triggering of this diatom’s sexual reproduction (auxosporulation) have been evidenced, such as cell concentration, light quality or light conditioning. In the aim of a European project, new species of blue diatoms have been discovered : Haslea silbo sp. nov. from the Canary Islands, Haslea karadagensis sp. nov. from the Black Sea and Haslea provincialis sp. nov. from the Mediterranean Sea. A first molecular phylogeny of the genus Haslea has been made using three markers : ITS1-5.8S-ITS2, rbcL and cox1. Blue diatoms appeared to belong to a distinct cluster inside the genus. Availability of two H. ostrearia populations from France and Sweden, sexually compatibles but bearing differences in their cox1 sequences allowed studying the distribution and inheritance of the mitochondrial DNA during auxosporulation. Moreover, UV-visible spectrophotometry and Raman spectometry have been used for pigments’ characterization. Existence of distinct pigments in the newly described species led to the proposal of a chemotaxonomic classification. Finally, biological activities of marennine and H. karadagensis’ pigments have been studied in regards of their antibacterial and antiviral properties.