Dans les écosystèmes littoraux, les communautés microphytobenthiques sont soumises à des conditions environnementales qui peuvent être extrêmes en particulier en ce qui concerne l'intensité lumineuse. Les mécanismes de protection mis en place dépendent étroitement du type d'habitat où se développent ces communautés et cette thèse a pour objectifs d'analyser les caractéristiques de l'activité photosynthétique et les mécanismes de protection développés par des assemblages microphytobenthiques dans deux écosystèmes littoraux très différents : les vasières intertidales atlantiques de la Baie de L'Aiguillon (France) et la lagune côtière non tidale de Puck Bay dans la Mer Baltique (Władysławowo, Pologne). Pour réaliser ces objectifs, trois études ont été réalisées : (1) la description des communautés microphytobenthiques, (2) la caractérisation de leur activité photosynthétique et (3) l'analyse des mécanismes de photoinhibition et de photoprotection.La structure taxonomique du microphytobenthos a été décrite en se basant sur des observations en microscopie optique et sur la mesure des caractéristiques des pigments photosynthétiques par chromatographie liquide à haute performance (HPLC). L'activité photosynthétique a été étudiée par des méthodes de microrespirométrie volumétrique et de spectrofluorométrie de la chlorophylle a. Les mécanismes de photoinhibition et de photoprotection ont été étudiés par fluorométrie en modulation d'amplitude pulsée (PAM).Les résultats obtenus nous ont permis de montrer que :1) Les communautés atlantiques sont fortement dominées par des diatomées épipéliques, alors que le microphytobenthos de la Mer Baltique est plus diversifié et comporte, outre des diatomées, une large part de cyanobactéries,2) Les microphytobenthos atlantique est bien acclimaté à des valeurs d'intensités lumineuses plutôt faibles, alors que les communautés de la Mer Baltique ont encore une bonne activité photosynthétique à de fortes irradiances,3) Les diatomées atlantiques présentent une plus forte photoinhibition que les microalgues de la Baltique,4) L'activité photosynthétique des communautés microphytobenthiques non perturbées montre un des rythmes circadien et tidal, qui semblent être contrôlés par des facteurs endogènes, qui mettent en jeu des adaptations comportementales comme la migration verticale pour les diatomées atlantiques,5) En ce qui concerne le microphytobenthos de la Mer Baltique, qui n'a pas de capacité migratoire, la photoprotection est assurée en premier lieu par la mise en jeu de processus physiologiques. Nous avons pu montrer la très grande flexibilité du photsystème PSII qui est capable de suivre très rapidement les changements à court terme de lumière ambiante. / The scope of this thesis includes the characteristics and comparison of photosynthetic activity and photoprotection mechanisms of microphytobenthos assemblages inhabiting the Atlantic intertidal mudflats of Aiguillon Bay (Esnandes, France) and the littoral zone of the Baltic Sea in non-tidal Puck Bay (Władysławowo, Poland). In order to accomplish the main aims of the work the following tasks were carried out: (1) characterization of microphytobenthic assemblages; (2) characterization of their photosynthetic activity and (3) description of photoinhibition and photoprotective mechanisms. The structure of microphytobenthos was described based on observation of the material in light microscope (LM) and through the characteristics of photosynthetic pigments using high performance liquid chromatography (HPLC). Photosynthetic activity was described using various methods including classical (volumetric micro-respirometer) and modern (chlorophyll a fluorescence) ones. In addition, the measurements of variable fluorescence were also used to study photoinhibition and photoprotective mechanisms. Based on the obtained results it was stated that:1.) the Atlantic assemblages were strongly dominated by epipelic diatoms, while the Baltic microphytobenthos was more diverse and cyanobacteria, next to diatoms, were also very important component,2.) it was shown that the Atlantic microphytobenthos was well acclimated to rather low light intensities, while the Baltic assemblages showed good utilization of higher irradiance,3.) the Atlantic diatoms were more susceptible to photoinhibition than the Baltic microalgae,4.) the photosynthetic activity described for the undisturbed microphytobenthos communities revealed circadian and circatidal rhythms, which seemed to be controlled by endogenous factors, supporting diatoms’ behavioural adaptations i.e., vertical migration,5.) in case of the Baltic microphytobenthos, the lack of the ability to move caused their physiological processes the first line of defence against excess irradiances. The analysis revealed extreme flexibility of PSII which was able to follow rapidly the short-term changes in ambient light

Abstract Understanding of natural and human induced changes to freshwater biodiversity patterns is critical for efficiently conserving and managing these highly impacted ecosystems. In this doctoral thesis, I study the natural spatial and temporal variability of littoral macroinvertebrate communities, as well as aquatic biodiversity responses (of bryophytes, macroinvertebrates and diatoms) to human impact on forested headwater streams. I also study the temporal variability of natural and human-impacted stream communities. I show that littoral macroinvertebrate communities are most variable between individual samples and to some extent between littorals, and that the diversity patterns of rare and common littoral macroinvertebrates vary at different spatial scales. Temporal (interannual) variability is of minor importance, particularly for the core species of the community. For rare species, however, the temporal component was generally more important than spatial turnover. For headwater streams, I show that most taxonomic groups responded negatively to human impact on the adjacent riparian forest. Nevertheless, pristine riparian forest is not a sufficient surrogate for stream biodiversity as also streams with relatively disturbed riparian forests supported diverse benthic communities. A rapid classification method based on the physical structure of the stream channel and its riparian forest is able to identify the reference-state communities, as well as the most severely altered communities, but a reliable identification of the intermediately-disturbed sites would need more precise information about the key stressors of stream communities. I found that fine sediments originating from forest drainage were the main factor causing reduction of stream biodiversity. I also found that forestry impacted streams varied temporally more than pristine streams, emphasizing the importance of interannual sampling of impacted streams for a reliable status assessment. / Tiivistelmä Luonnollisen ja ihmisen aiheuttaman biodiversiteettivaihtelun ymmärtäminen hoito- ja suojelutoimissa on tärkeää pienvesien monimuotoisuuden turvaamiseksi. Tarkastelen väitöskirjassani järvien rantavyöhykkeen pohjaeläinten ajallista ja paikallista vaihtelua sekä latvapurojen eliöyhteisöjen (pohjaeläimet, sammalet, piilevät) vasteita ihmisen aiheuttamaan fysikaaliseen muutokseen rantametsässä ja purouomassa. Tarkastelen myös ajallisen vaihtelun eroja luonnontilaisten ja ihmisvaikutteisten latvapurojen eliöyhteisöjen välillä. Osoitan, että järven rantavyöhykkeen pohjaeläinyhteisöt vaihtelevat eniten yksittäisten näytteiden välillä ja pienessä määrin eri rantojen välillä, mutta ajallinen vaihtelu ei heikennä tulosten luotettavuutta muiden kuin harvinaisten lajien osalta yhteen vuoteen rajoittuvassa näytteenotossa. Purotutkimuksissa osoitan, että useiden vesieliöryhmien lajirunsaus muuttuu ihmisen aiheuttaman rantametsän muutoksen seurauksena, mutta luonnontilaista rantametsää ei silti voida pitää yksiselitteisesti myös puron suojelutason mittarina, koska se ei välttämättä turvaa eliöiden lajistollista eheyttä suhteessa alkuperäiseen alueelliseen lajistoon. Rantametsän ja uoman fysikaalisiin rakennepiirteisiin perustuvaa nopeaa luokittelumenetelmää voidaan käyttää eliöyhteisöltään monimuotoisimpien ja metsätalouden voimakkaimmin rasittamien purojen tunnistamisessa. Eliöyhteisöltään lievemmin muutettujen purojen luotettavaan erotteluun luokittelun pitäisi kuitenkin sisältää tarkempaa tietoa metsäojitusten aiheuttamasta liettymisestä, joka on tulosteni perusteella haitallisin metsätaloudesta johtuva puroyhteisöjä rasittava tekijä. Havaitsin myös metsätalouden rasittamien purojen tilanarvioinnin toistettavuuden olevan luonnontilaisia puroja heikompaa, joten metsätalouden rasittamien purojen pidempiaikainen seuraaminen tuntuu välttämättömältä luotettavien tilanarvioiden tuottamiseksi.

Durant les dernières décennies, la Péninsule Antarctique a été identifiée comme étant la région où le réchauffement récent est le plus marqué dans l’Hémisphère Sud. Cependant, au-delà de la période instrumentale, la variabilité climatique Holocène de cette partie du globe est en grande partie inconnue. Cette absence de données limite notre capacité à évaluer les l’amplitude des changements actuels dans le contexte de la variabilité historique ainsi que les mécanismes de forçage sous-jacents. Nous avons ainsi ciblé nos analyses sur des enregistrements sédimentaires prélevés à l’Est et à l’Ouest de la Péninsule Antarctique, avec pour objectif d’étendre les connaissances spatiales et temporelles des conditions de l’océan de surfaces dans ce secteur de l’Antarctique au cours du dernier siècle, du dernier millénaire ainsi que durant l’Holocène. La méthodologie de cette thèse est basée sur une comparaison multi-proxies qui inclut, comme outils principaux, les assemblages des diatomées et les biomarqueurs spécifiques de diatomées (HBIs). Nous avons pu ainsi documenter la réponse régionale environnementale aux variations climatiques à différentes échelles de temps, et définir les mécanismes forçant sur la variabilité des conditions d’océan de surface ainsi que la formation du couvert de banquise en Péninsule Antarctique. La comparaison de nos enregistrements avec des données issues des carottes de glace, a permis de mettre en évidence le rôle important des changements d’intensité des cellules atmosphériques sur la dynamique de la circulation océanique, la durée du cycle saisonnier de banquise et la productivité siliceuse. / The Antarctic Peninsula has been identified during the last decades as the region from the Southern Hemisphere which is the most affected by the recent warming. However, beyond the instrumental period, the Holocene climate variability of this area is largely unknown, limiting our ability to evaluate the current changes within the context of historical variability and underpin the underlying forcing mechanisms. We focused our analysis on sedimentary sequences from the Eastern and Western side of the Antarctic Peninsula, in order to expand the spatial and temporal knowledge of sea-surface conditions over the last century, the last millennium and throughout the Holocene in this Antarctic area. The inferences are based on a multi-proxy comparison mainly using diatom assemblages and diatom specific biomarkers (HBIs). We documented the regional environmental response to climate changes at different time scales and described the forcing mechanisms on the sea-surface conditions and sea ice cover variability in Antarctic Peninsula. Comparing our results with ice core data allowed us to highlight the large impact of atmospheric forcings on the oceanic circulation, the seasonal sea ice dynamics and the siliceous productivity.

Les diatomées sont des algues microscopiques qui sont largement utilisées pour évaluer la qualité écologique des cours d'eau.Les méthodes utilisées se basent sur des modèles simplifiés de biologie des communautés, dans lesquels seules les réponses individuelles des espèces à l'environnement sont prises en compte.Le test de l'importance de processus complémentaires a montré un impact fort des dynamiques de colonisation des espèces, mais un impact négligeable des phénomènes de compétition ou de facilitation.Ces processus impliquent une structure des assemblages bien plus complexe que celle habituellement assumée par les méthodologies de bioindication.L'adaptation et la mise en oeuvre de méthodes de réseaux de neurones et de logique floue nous ont permis de redéfinir des éco-régions françaises et de décrire des relations générales entre les traits biologiques des espèces et l'environnement, tout en prenant mieux en compte cette complexité. / Diatoms are microscopic algae which are widely used to monitor the ecological quality of strems and rivers. The regular methodologies are based on simpllified community models. In these models, only the invidual species responses to environment are accounted for.Testing the importance of complementary processes showed a significant effect of colonization dynamics, but only a slight effect of biotic relationships. These processes led us to considerate a more complex assemblage structure than the one usually assumed by the biomonitoring methodologies.Therefore we implemented both neural networks models and fuzzy logic methodologies, in order to refine French ecoregions and to describe relationships between species traits and environment.

The aim of this thesis has been to reconstruct paleoenvironment, paleohydrology and paleoclimate in coastal southern Mozambique, with emphasis on tracing past flooding events on the lower Limpopo River floodplain. In order to extend flood chronologies beyond periods covered by instrumental data, sediments from lakes on the floodplain were studied (Lake Lungué, Coassane Oxbow, Lake Magandane and Lake Soane). Past sea-level variations and climate changes were deduced by analyzing sediments from coastal sites north of the floodplain area (Lake Chilau, Lake Nhauhache and Macassa Bay). To achieve the established objectives, a multi-proxy approach was applied on most of the retrieved sediment cores, involving analysis of mineral magnetic parameters, grain-size and organic carbon in combination with analysis of microfossils such as diatoms and/or phytoliths. Chronologies for the constructed time-series analysis were obtained by radiocarbon dating and age-depth modelling. The synthesized data from the sampled sites on the Limpopo River floodplain suggest that the area was affected by at least 16 flooding events of variable magnitudes during the studied period. These are dated to c. AD 940, 980, 1040, 1100, 1250, 1300, 1370, 1580, 1665, 1730, 1755, 1855, 1920, 1945, 1970 and 2000. In calibrated years BP these ages correspond to 1010, 970, 910, 850, 700, 650, 580, 370, 285, 220, 195, 95, 30, and 5 cal yrs BP. The two youngest are dated to 20 and 50 years AP (After Present being 1950). Proxy data further suggest that southern Africa was subject to two periods of sea-level highstands, at c. 5000–4200 BC (6950–6150 cal yrs BP) and AD 300–950 (1650–1000 cal yrs BP). The former represents the middle part of the postglacial climatic optimum. The wettest period in the Limpopo River floodplain was reported between AD 1360 and 1560 (590 and 390 cal yrs BP) in the Lake Lungué record, while Lake Chilau experienced wet conditions between AD 1200 and 1400 (750 and 550 cal yrs BP), then returning to drier conditions that prevailed until c. AD 1600. In Lake Nhauhache, however, drier conditions prevailed from c. AD 1200–1700 (750–250 cal yrs BP), shifting towards wetter at c. AD 1900 (50 cal yrs BP). The deviating signals between records can partly be explained by Lake Lungué basin being located on the Limpopo River floodplain, responding to flooding events associated with precipitation upstream the drainage area. Therefore, wet and dry periods in floodplain lakes (e.g. Lake Lungué) are not expected to correlate with precipitation changes on a local scale, as indicated by e.g. Lake Nhauhache. This is supported by a relatively weak agreement between Lake Lungué record and other nearby records (outside the floodplain), but a better correlation with records from the upper catchment, where a more regional climate signal is provided of the southern African summer rainfall region. / Denna avhandling behandlar studier av paleomiljöer i södra Mozambique med fokus på översvämningshistorik i Limpopo-flodens nedre lopp. Tidsspannet är mitt- och sen-holocen och inkluderar även klimat och havsnivåvariationer. Följande analysmetoder har applicerats på ett flertal sedimentkärnor för att belysa ovanstående frågeställningar: mineralmagnetiska parameterar, kornstorlek, organiskt kol samt kiselmikrofossil (diatoméeter och fytoliter). Åldrar har bestämts med 14C-metoden.  Analyserna visar att mineralmagnetiska parametrar är lämpliga för att identifiera översvämningar, speciellt magnetisk susceptibilitet och SIRM. Dessa parametrar visar på ett sediments magnetiska kornstorlerkar och koncentrationen av finkorniga magnetiska mineral. Även kornstorleksanalyser fungerade som ett bra komplement till dessa metoder. Sammantaget har ett minimum av 16 översvämningar registrerats i Limpopo/flodens nedre lopp under de senaste 1100 åren. Särskilt stora översvämningar har daterats till AD 1250 (700 kal år BP), AD 1370 (580 kal år BP), AD 1580 (370 kal år BP), AD 1855 (95 kal år BP), AD 1920 (30 kal år BP), AD 1970 (20 kal år AP) och AD 2000 (50 kal år AP), där AP betyder ”after present”, vilket är 1950. Mindre kraftiga översvämningar har daterats till AD 940 (1010 kal år BP), AD 980 (970 kal år BP), AD 1040 (910 kal år BP), AD 1100 (850 kal år BP), AD 1300 (650 kal år BP), AD 1665 (285 kal år BP), AD 1730 (220 kal år BP), AD 1755 (195 kal år BP) och AD 1945 (5 kal år BP). Skriftliga källor visar på att åtminstone åtta översvämningar har ägt rum under de senaste 62 åren. Under samma period har denna undersökning registrerat två händelser, vilket indikerar att endast ett fåtal har registrerats med ovan nämnda metoder. Det är sannolikt att sedimentationsmönstret under en översvämning är komplicerat och inte heller likartad från gång till gång. Detta innebär att ett flertal sedimentkärnor behöver analyseras och dateras väl. Ytterligare en försvårande faktor är flodens mycket aktiva meandringsaktivitet. Analys av diatoméer har visats vara värdefulla när det gäller översvämningshistorik, klimatförändringar och havsytevariationer. Sedimenten i den något till flodslättens nedre lopp perifert belägna sjön Lungué indikerar fuktiga förhållanden mellan AD 1360 och 1560 (590 till 390 kal år BP). Kombinerade fytolit- och diatoméanalyser av sedimenten i sjön Chilau indikerar fuktiga förhållanden från AD 1200 till 1400 (750 till 550 kal år BP), varefter torrare förhållanden rådde till ca AD 1600 (350 kal år BP). Diatoméanalys av sedimenten i sjön Nhauhache indikerar generellt sett torrare förhållanden mellan AD 1200 och AD 1700 (750 till 250 kal år BP) då klimatet blev fuktigare. De fuktiga och torra förhållanden som dokumenterats i sjön Lungué och översvämningshistoriken korrelerar inte helt med lokala nederbördsförhållanden. Däremot stämmer erhållna data bättre med förhållanden i den övre delen av Limpopoflodens dräneringsområde. Även sjöar och fyllda meanderbågar på själva flodslätten verkar reagera tydligare på översvämningar orsakade av nederbörd i den övre delen av flodloppet. Undersökningen indikerar två faser av en förhöjd havsyta längs kusten i södra Mozambique. En äldre fas är daterad till ca 5000–4200 f.Kr. (6950–6150 kal år BP), vilken representerar den mellersta delen av det postglaciala värmeoptimet. Denna tolkning stöds även av andra undersökningar. En yngre fas har daterats till AD 300–950 (1650–1000 kal år BP), vilken korresponderar till en period med något förhöjda temperaturer i ett globalt perspektiv. / O presente projecto teve como objectivo a reconstrução do paleoambiente, paleohidrologia e paleoclima da costa Sul de Moçambique, com ênfase na identificação de vestígios de eventos de cheias que tenham, no passado, afectado a planície de inundação do Rio Limpopo, com vista a fazer a extensão das datações de cheias para o período anterior aos instrumentos de medição. Deste modo, foram estudados sedimentos recuperados através de testemunhos de sondagem em lagos dentro da planície de inundação (Lago Magandane, Lago Lungué, Lago Soane e o canal abandonado Coassane). As variações do nível do mar e mudanças climáticas do passado foram deduzidas a partir da análise de sedimentos de áreas costeiras a norte da planície de inundação (Lago Chilau, Lago Nhauhache e a Baía de Macassa). Para o alcance destes objectivos, os sedimentos dos testemunhos de sondagem recuperados foram submetidos a várias análises laboratoriais que incluem propriedades de minerais magnéticos, granulometria, teor de matéria orgânica e de microfósseis (diatomáceas e fitólitos). Para o estabelecimento do modelo cronológico foram usadas datações pelo método 14C feitas em matéria orgânica, assim como conchas de gastrópodes e bivalves. A combinação dos resultados obtidos para os pontos de amostragem localizados dentro da planície de inundação do Rio Limpopo, sugerem que esta área foi afectada por um mínimo de 16 eventos de cheias de variada magnitude nos últimos 1100 anos. As cheias de alta magnitude tiveram lugar nos anos 1250, 1370, 1580, 1855, 1920, 1970 e 2000. Por seu turno, as cheias de magnitude moderada ocorrerram nos anos 940, 980, 1040, 1100, 1300, 1665, 1730, 1755 e 1945.. Os anos a negrito são indicativos de eventos de cheias de alta magnitude. O número total de eventos identificados no presente estudo é um mínimo que poderá ter afectado a planície de inundação, tendo em consideração que fontes escritas reportam a ocorrência de pelo menos oito eventos nos últimos 62 anos, tendo o presente estudo revelado somente dois. Isto indica que apenas eventos de cheias intensos podem ser revelados pelos métodos aplicados nesta investigação. Adicionalmente, este estudo mostra a necessidade de aumentar o número de pontos de amostragem para permitir a identificação de mais eventos de cheias ocorridos no passado, devido à diferenciada resposta sedimentológica e geomagnética às cheias, a qual se encontra directamente relacionada à distância do rio meandrante. As análises de microfósseis de diatomáceas permitiram reconstruir o paleoclima e as influências do nível do mar nas áreas de estudo deste projecto. Os registros de diatomáceas do Lago Lungué indicam um período húmido entre AD 1360 e 1560. No Lago Chilau, dados de diatomáceas e fitólitos sugerem condições de humidade entre AD 1200 e 1400. Por seu turno, no Lago Nhauhache, condições de seca dominam entre AD 1200 e 1700. As condições de seca e humidade documentadas no Lago Lungué e os eventos de cheias revelados pelos sedimentos analisados da planície de inundação do Rio Limpopo não mostram total correlação com períodos de baixa e alta precipitação a nível local, mas apresentam boa correlação com evidências a montante na área de drenagem do Rio Limpopo. Em geral, lagos activos ou preenchidos por sedimentos mostrarão ser mais susceptíveis a cheias com origem a montante do que a nível local. As investigações conduzidas permitiram identificar dois períodos de alto nível do mar na região sul de Moçambique. A fase mais antiga teve lugar há cerca de 5000–4200 BC (6950–6150 anos do calendário BP), representando a fase mais recente do pós-glaciar climático óptimo (postglacial climatic optimum, PCA). A fase recente é datada de AD 300–950 (1650–1000 anos do calendário BP), correspondendo a um período de temperaturas relativamente altas a nível global. / Climate and Environmental Research

Les cycles biogéochimiques du carbone et des éléments biogènes (Si, N, P) ont été étudiés en lien avec la dynamique nutritionnelle du phytoplancton dans le système naturellement fertilisé des Kerguelen. Cette étude s'inscrit dans le programme KEOPS2, qui a ciblé le nord-est du plateau des Kerguelen au début de la saison productive. La comparaison avec une zone HNLC limitée en fer a confirmé certaines des précédentes observations réalisées au cours des expériences de fertilisations artificielles et naturelles : le fer stimule clairement la croissance du phytoplancton et plus particulièrement celle des diatomées. Les zones naturellement fertilisées se sont en effet caractérisées par des biomasses en chlorophylle a et en silice biogénique 3-10 fois supérieures à la zone non-fertilisée et, par de fortes vitesses de production de silice biogénique atteignant des valeurs rarement observées dans l'océan Austral. La zone HNLC s'est caractérisée quant à elle par une population nanoplanctonique principalement composée de nanoflagellés autotrophes non siliceux. Ces travaux soulignent l'importance d'étudier la composition spécifique des populations de diatomées pour comprendre leurs implications dans les cycles du C et du Si. Nos observations ont montré que les caractéristiques physiologiques des diatomées conditionnent directement l'export de matière en profondeur dans la région des Kerguelen. Cette idée a notamment été illustrée par l'étude de l'évolution saisonnière du bloom au sud-est du plateau. / Biogeochemical cycles of carbon, silicon, nitrogen and phosphorus were studied in relation to the nutritional dynamics of phytoplankton in the naturally iron-fertilized region of Kerguelen, in the Southern Ocean. This study was conducted in the framework of the KEOPS 2 program which took place in the northeastern part of the Kerguelen Plateau in early austral spring (October-November 2011). The comparison between this iron-fertilized region and an iron-limited HNLC (High Nutrient Low Chlorophyll) area confirmed some previous observations from artificial and natural fertilization experiments: iron availability clearly stimulates phytoplankton growth and especially diatom growth. Iron-fertilized regions were characterized by 3-10 fold higher chlorophyll a and biogenic silica biomasses than the iron-limited area, as well as higher biogenic silica production rates reaching values rarely observed in the Southern Ocean. The HNLC area was characterized by a nanoplanktonic assemblage mainly composed of non-siliceous autotrophic nanoflagellates. Our results highlight the importance of studying the specific composition of diatom assemblages to better understand their impact on the C and Si biogeochemical cycles. Our observations showed that physiological traits of diatoms directly drove matter export to depth in the Kerguelen region. This idea was illustrated through the seasonal evolution of the south-eastern bloom by combining our data with KEOPS 1 data. In this region, a shift in the diatom assemblage was observed in parallel to an evolution of the vertical flux of matter, and of uptake and particulate matter ratios Si:C:N.

Les travaux présentés dans ce manuscrit portent sur l’étude des propriétés photoniques de quatre espèces de diatomées du genre Coscinodiscus : C. wailesii, C. specie, C. radiatus et C. radiatus-cf. Les diatomées sont des micro-algues unicellulaires constituées d’une cellule unique encapsulée dans une matrice inorganique de silice poreuse appelée frustule. Nous avons effectué des cultures de ces espèces, puis extrait les frustules afin de les caractériser, tant du point de vue de leur composition que de leur morphologie, par microscopie électronique et tomographie RX. Le frustule est constitué de trois couches de silice (le foramen, le cribrum et le cribellum) présentant une structure poreuse hiérarchique, s’étendant du micromètre au nanomètre, et formant ainsi une matrice tridimensionnelle complexe pouvant présenter des propriétés photoniques. Le foramen et le cribrum présentent des réseaux de pores de périodicité importante dont les dimensions caractéristiques (taille des pores, pas du réseau…) sont de l’ordre de grandeur des ondes lumineuses. Les propriétés optiques des frustules ont alors été étudiées expérimentalement par imagerie spectrale et théoriquement par simulations numériques par la méthode des éléments finis. Nous avons ensuite mis en évidence un effet de concentration de la lumière visible transmise sur l’axe de la diatomée à quelques dizaines de micromètres derrière le frustule. Cet effet s’avère dépendre de la longueur d’onde incidente ainsi que de l’orientation du frustule. Finalement, nous avons montré, par approche théorique et simulations numériques, que cet effet de concentration de la lumière le long de l’axe est majoritairement dû au foramen et que les autres couches n’ont qu’un effet marginal. Une telle micro et nano-structuration complexe de la matière est actuellement inaccessible à l’échelle industrielle. Cette structure présente cependant des effets de concentration et de filtration des ondes lumineuses d’un grand intérêt dans de nombreux domaines (photovoltaïque, cosmétique, peinture…) et on peut donc envisager raisonnablement une utilisation directe des diatomées. / The work presented in this thesis deals with the study of the photonic properties of four diatom species of the genus Coscinodiscus: C. wailesii, C. specie, C. radiatus et C. radiatus-cf. Diatoms are unicellular microalgae consisting of a single cell encapsulated in an inorganic matrix of porous silica called frustule. We performed cultures of these species, then extracted the frustules to characterize them, both in terms of their composition and their morphology, by electron microscopy and X-ray tomography. The frustule consists of three silica layers (the foramen, cribrum and cribellum) with a hierarchical porous structure, ranging from micrometer to nanometer scale, and thus forming a complex three-dimensional matrix that may have photonic properties. The foramen and cribrum have periodic pores networks whose characteristic dimensions (pore size, lattice constant…) are of the order of light wavelengths. The optical properties of the frustules were then studied experimentally by spectral imaging and theoratically by numerical simulations by finite element method. We demonstrated a concentration effect of visible light transmitted on diatom’s axis a few tens of micrometers behind the frustule. This effect appears to depend on the incident wavelength as well as the orientation of the frustule. Finally, we have shown by theoratical approach and numerical simulations, that light concentration effect along the axis is mainly due to the foramen and the rest of layers have only a marginal effect. Such complex micro and nano-structuring of matter is currently impossible on an industrial scale. This structure, however, has optical effects of light concentration and filtration of great interest in many fields (photovoltaics, cosmetics, paint…) and it is therefore reasonnable to consider a direct use of diatoms.

Diatom analysis of basal part of profile PK-1-L contributes to multi-proxy research of former Lake Komořany. At this part of profile radiocarbon dating (dates sediments into Late Glacial and Early Holocene) and LOI (loss on ignition) had been conducted before, of which results have been utilized to more accurate interpretation of diatom analysis conclusions. Apart from diatom valves, presence of stomatocysts of Chrysophyceae has been observed. Having separated diatom valves from 32 sediment samples in intervals 0,4-0,6 cm, permanent preparates have been created. Concentration of valves in a gramme of dry sediment and relative abundance of diatom taxons in each sample have been investigated using light microscopy. In a half of samples subdominants and rare taxons have been observed separately to eliminate the interference from dominant taxons. Cluster analysis based on relative abundances of diatom taxons have been calculated and on its results have been subsequently determined three diatom accumulation zones (DAZ). Moreover trophic and saprobic indices have been calculated and levels of pH, conductivity and concentration of total phosphorus (TP) have been estimated by transfer functions. Even before beginning of Holocene the major shift in composition of diatom communities have happened, to the...

Since the 18th-century scientists are studying diatoms, fascinated by their beauty and diversity. Their nano- and micropatterned biosilica cell walls are outstanding examples of biologically controlled mineral formation. Although the knowledge about diatom cell wall formation increased over the last 60 years, the process is still far away from being completely understood. Diatom cell walls exhibit highly interesting material properties, making them appealing to material scientists. Due to those properties, diatom cell walls are on the brink of becoming powerful tools in nanotechnology. However, the production of tailored silica structures for nanotechnology requires a much better understanding of the processes and components involved in cell wall morphogenesis. Recent studies set the focus on insoluble organic matrices as important parts of this process, suggesting that they act as templates in silica morphogenesis. Therefore, in this study, the occurrence of insoluble organic matrices and their possible silica precipitation activity was analyzed in the three diatom species T. pseudonana, T. oceanica and C. cryptica. For all three species girdle band and valve derived insoluble organic matrices could be identified. The extracted insoluble organic matrices exhibited structural features present in the corresponding biosilica cell walls. The highest similarities were found in the valve derived matrices of C. cryptica. Accessibility studies showed that the biosilica associated insoluble organic matrices of T. pseudonana were only partially accessible, arguing for an entrapment of insoluble organic matrices in the silica, rather than an attachment to the surface of the cell wall. All examined insoluble organic matrices of the three species exhibited intrinsic silica precipitation activity. The most intriguing structures were formed by the insoluble organic matrices of C. cryptica, yielding a porous silica pattern. The addition of biosilica derived soluble components or long-chain polyamines promoted this process and moreover lead to the reconstitution of biosilica-like hierarchical silica pore patterns. The generated silica structures were templated by the underlying structure of the insoluble organic matrix. The result presented in this thesis make this the first study reporting the in vitro generation of diatom biosilica-like hierarchical silica pore patterns using all natural cell wall components. It supports the hypothesis of microplates acting as templates for biosilica morphogenesis and introduces an interesting experimental setup for silica-based in vitro studies on the mechanism of pore formation in diatoms.

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