S'han estudiat els efectes dels factors ambientals sobre el perífiton dels sistemes lenític fluctuants del aiguamolls de l'Empordà. L'estudi s'ha realitzat als tres nivells d'integració: nivell d'ecosistema considerant el rol del perífiton envers els altres productors primaris; a nivell de comunitat, estudiant la composició específica de les diatomees i a nivell de població estudiant la plasticitat fenotípica d'una espècie de diatomea (Nitzschia frustulum).A nivell d'ecosistema s'observa que els factors que afavoreixen el predomini dels diferents tipus de productors primaris (perífiton, fitoplàncton i macròfits) són la renovació i el grau d'eutròfia de l'aigua. A nivell de comunitat els factors determinants en la composició i distribució de les espècies de diatomees són els gradients confinament-inundació així com la productivitat del sistema. En funció d'aquest factors s'han establert 5 associacions de diatomees. A nivell de població es demostra que tant la salinitat, com la relació N : P a l'aigua com el moviment de l'aigua afecten la morfologia i ultraestructura de la valva de N. frustulum. De forma interessant s'observa que la salinitat, considerada com a factor individual, afecta N. frustulum a nivell poblacional provocant-li modificacions en la morfologia de la valva, per en canvi, no afecta a nivell de comunitat, ja que totes les espècies de diatomees presents en ambients de salinitat fluctuant són eurihalines. / The effects of environmental conditions on periphytic of lentic and fluctuating waters (Empordà wetlands) at the three different levels of organisation were studied: at ecosystem level, considering the role of periphyton among the primary producers; at community level, analysing the periphytic diatom species composition; and at population level studying the phenotypic plasticity of a selected diatom species (Nitzschia frustulum). The factors favouring the predominance of different primary productors (periphyton, phytoplankton and macrophytes) were the turnover and eutrophy of the water. At the community level, we observed that the main factors affecting diatom species composition and distribution are the gradients confinement-flooding and productivity of the system. Based on these factors 5 diatom assemblages have been distinguished. At the population level, the results of the present thesis proved that the morphology and ultrastructure of N. frustulum is affected by salinity, N : P ratio and movement of the water. Interestingly the results showed that salinity, as a single environmental factor, has effect at N. frustulum population level resulting in phenotypic plasticity while there is no effect of salinity at diatom community level since in such environments with fluctuating salinity all the species present are euryhaline.

Microphytobenthos (MPB), a mixed community of microscopic, photosynthetic organisms, algae and cyanobacteria, inhabiting the top few millimetres of bottom sediment, is a key component of intertidal mudflats. It accounts for a significant proportion of estuarine primary production, forms the base of the food chain and influences sediment distribution and resuspension (through production of extracellular polymeric substances (EPS)). Diatoms dominate the microphytobenthos community in the mid-latitudes of the Northern Hemisphere. Estuarine sediments, are a sink for metal contaminants derived from fluvial, marine and atmospheric sources. Whilst metal releases to estuaries have declined in recent years due to increased regulation and declining industrial activity, metals previously discharged and which are now locked up in saltmarsh sediments remain a concern. For example, there are indications that saltmarshes are already being eroded, due to climate change related sea level rise, in some locations. This erosion may result in the redistribution of historically contaminated sediment to locations, such as the mudflats, where it is more available to biota, such as the MPB. In addition to causing redistribution, climate change effects, such as increasing temperatures and storminess, may also alter the bioavailability of metals to MPB. Increased concentrations of metals within the MPB could potentially increase their transfer to higher organisms through the food chain with potential impacts for biota. Whilst planktonic algae have been well studied with respect to metal uptake from the water column, there has been little research involving MPB and uptake of metals from sediment. The extent to which contaminant uptake by microphytobenthic algae occurs and under what conditions is therefore poorly understood. The research presented uses laboratory, mesocosm and field studies, to gain an understanding of processes governing metal bioavailability and mechanisms for uptake from sediment to the diatoms of the MPB under the complex and variable conditions of intertidal mudflats. A laboratory study using a single diatom species Cylindrotheca closterium found that uptake of cadmium (Cd) varied with sediment properties revealing the importance of sediment particle size and organic matter content in metal bioavailability to diatoms. Additionally, this study showed that the presence of diatoms altered Cd partitioning between sediment, overlying and pore water. Specifically there was an increase in Cd in the overlying and pore water when diatoms were present, indicating that diatoms mobilise metals from the sediment to the water column potentially increasing metal bioavailability to other biota. A study was conducted using an intertidal mesocosm to increase the realism of the study system and examine uptake to a natural MPB community. Diatoms were found to have higher concentrations of all the metals analysed (except tin) than other types of algae (filamentous and sheet macroalgae), confirming their importance as a study organism with respect to metal uptake and potential mobilisation through the food chain. Sediment disturbance was shown to increase metal uptake (iron, aluminium, vanadium and lead) from the sediment to algae. This is of concern due to predicted increases in storminess which are likely to increase sediment disturbance, with the likelihood that uptake of metals to diatoms will increase in the future. However, there were also indications of an antagonistic effect of temperature on disturbance, whilst disturbance increased bioavailability and uptake, increasing temperatures reduced uptake of some metals. This highlights the importance of considering the effects of multiple stressors in complex systems. Field studies showed that concentrations of some metals were related to their position on the mudflat whilst others were related to sampling date, indicating that there may be seasonal controls, such as to the presence of greater diatom biomass in spring and autumn, on metal uptake from the sediment. The research conducted has increased understanding of metal uptake to microphytobenthic diatoms from sediment and the influence they have in transferring metals from sediment to water, however the research also raises a number of new questions. For example, there appeared to be a link between sediment organic matter content and bioavailability of metals to diatoms, although the relative contribution of the diatoms, other algae, cyanobacteria and EPS to the sediment organic matter warrants further investigation. Furthermore, it has shown that the use of laboratory and mesocosm studies for this type of research can produce similar outcomes to those observed in the field but under more controlled and easily manipulated conditions, although field studies will continue to be vital in improving understanding of metals availability and transfer.

Typescript. Includes vita and abstract. Bibliography: Includes bibliographical references (leaves 79-83). Description: viii, 83 leaves : ill., map ; 29 cm.

Ces travaux s’intéressent au comportement de pâtes de ciment de différentes natures cimentaires exposées à une eau douce naturelle et plus particulièrement aux interactions avec les éléments biologiques. Cette étude est basée sur l’analyse comparative d’échantillons placés en milieu naturel (Moselle) et en milieux artificiels de laboratoire. Quels que soient les milieux et les microorganismes considérés, les résultats montrent une modification de la minéralogie de la surface et du réseau poreux des échantillons (taux de porosité, propriétés de transferts). Les essais en laboratoire ont permis d’isoler l’influence spécifique des bactéries dans les phénomènes de biolixiviation. Le dénombrement bactérien montre aussi que la densité de cellules présentes dans le biofilm recouvrant les échantillons dépend peu de la nuance cimentaire, excepté pour les ciments au calcaire. Les observations au MEB ont révélé, sur l’ensemble des échantillons, la présence abondante de diatomées en partie recouvertes par une couche minérale issue d’une cristallisation secondaire. La colonisation de la surface par ces diatomées est influencée par la géométrie et la nature minéralogique des échantillons. Les résultats d’essais en laboratoire ont montré qu’elles ont des interactions avec la pâte de ciment, l’évolution des densités de population de diatomées coïncide en effet avec l’évolution des caractéristiques de porosité (taux de porosité, propriétés de transferts) / This work focuses on the behavior of cement pastes of different cement bases exposed to natural fresh water and on the interactions with the biological elements. This study is based on the comparative analysis of samples immersed in natural environment (Moselle) and in artificial laboratory media. Whatever the media and microorganisms considered, the results show a change in the mineralogy of the surface and the porous network of the samples (porosity rate, transfer properties). Laboratory tests highlighted the specific influence of bacteria in bioleaching phenomena. The bacterial count also shows that the density of cells present in the biofilm covering the samples does not mainly depend on the cementitious grade, except for the limestone cements. The SEM observations revealed the abundant presence of diatoms on all samples. Diatoms are partly covered by a mineral layer resulting from secondary crystallization. The colonization of the surface by these diatoms is influenced by the geometry and mineralogical nature of the samples. The results of laboratory tests have shown that they interact with cement paste; the evolution of diatom population densities coincides with changes in porosity characteristics (porosity rate, transfer properties)

Submitted by Biblioteca de Pós-Graduação em Geoquímica BGQ (bgq@ndc.uff.br) on 2017-11-01T15:59:40Z No. of bitstreams: 1 Dissertação _Anna Beatriz Jones Oaquim_Digital.pdf: 6278668 bytes, checksum: 60236079c59e16ffdb171fe240dd8a21 (MD5) / Made available in DSpace on 2017-11-01T15:59:40Z (GMT). No. of bitstreams: 1 Dissertação _Anna Beatriz Jones Oaquim_Digital.pdf: 6278668 bytes, checksum: 60236079c59e16ffdb171fe240dd8a21 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro / Universidade Federal Fluminense. Instituto de Química. Programa de Pós-Graduação em Geoquímica, Niterói, RJ / The use of diatoms as micropaleontological indicators has been used in the last decades, since these organisms that are sensitive to environmental changes, having their frustules preserved in the sediments, allow paleoenvironmental and / or paleoclimatic reconstructions. In this context, the present study aims to reconstruct regional climatic variations in the South Shetland Islands, located on the west coast of the Antarctic Peninsula, using a corer with 50cm sampled at the Glubokoe Deepe Proglacial Lake (62 ° 11,066'S, 58 ° 54,413'O), Fildes Peninsula, King George Island, based on the fossil record of diatoms. In qualitatively analysis on the sedimentary layers from the period 2013 to 1737, 34 taxa were found and identified, of which only 19 were considered as frequent. Among these 19 taxa the most abundant species along all layers was the centric diatom Aulacoseira glubokoyensis, a new species discovered throughout this study, followed by penate diatoms, which present a high diversity. Aulacoseira glubokoyensis showed a decrease in relative abundance and cell size in the period of higher ozone variation, probably associated to the adaptation to this environmental condition associated to the increase of UV-B radiation. Based on the correlations obtained between the environmental variables and the relative abundance of the frequent taxa, it was possible to establish three reconstruction models, one for temperature, the other for the average energy of cyclones occurring between 50 ° and 70 ° S and other for the minimum ozone content in the atmosphere. The first model of reconstruction was based on the relative abundance of Brachysira minor and Pinnularia sp. And presented an associated error of only 13%, the second in the relative abundance of Nitzschia cf. Kleinteichiana, Pinnularia borealis, Gomphonema sp. with an average error of 2% and the last one, of minimum ozone, was based in the relative abundance of Planothidium australe, Pinnularia borealis, Gomphonema sp. and Humidophila tabellariaeformis, with mean associated error of 11%. Thereby, for this region diatom assemblies can be used as paleoclimatic reconstructors / The use of diatoms as micropaleontological indicators has been used in the last decades, since these organisms that are sensitive to environmental changes, having their frustules preserved in the sediments, allow paleoenvironmental and / or paleoclimatic reconstructions. In this context, the present study aims to reconstruct regional climatic variations in the South Shetland Islands, located on the west coast of the Antarctic Peninsula, using a corer with 50cm sampled at the Glubokoe Deepe Proglacial Lake (62 ° 11,066'S, 58 ° 54,413'O), Fildes Peninsula, King George Island, based on the fossil record of diatoms. In qualitatively analysis on the sedimentary layers from the period 2013 to 1737, 34 taxa were found and identified, of which only 19 were considered as frequent. Among these 19 taxa the most abundant species along all layers was the centric diatom Aulacoseira glubokoyensis, a new species discovered throughout this study, followed by penate diatoms, which present a high diversity. Aulacoseira glubokoyensis showed a decrease in relative abundance and cell size in the period of higher ozone variation, probably associated to the adaptation to this environmental condition associated to the increase of UV-B radiation. Based on the correlations obtained between the environmental variables and the relative abundance of the frequent taxa, it was possible to establish three reconstruction models, one for temperature, the other for the average energy of cyclones occurring between 50 ° and 70 ° S and other for the minimum ozone content in the atmosphere. The first model of reconstruction was based on the relative abundance of Brachysira minor and Pinnularia sp. And presented an associated error of only 13%, the second in the relative abundance of Nitzschia cf. Kleinteichiana, Pinnularia borealis, Gomphonema sp. with an average error of 2% and the last one, of minimum ozone, was based in the relative abundance of Planothidium australe, Pinnularia borealis, Gomphonema sp. and Humidophila tabellariaeformis, with mean associated error of 11%. Thereby, for this region diatom assemblies can be used as paleoclimatic reconstructors

Made available in DSpace on 2014-07-29T16:21:22Z (GMT). No. of bitstreams: 1 Dissertacao Barbara Dunk Oliveira.pdf: 635497 bytes, checksum: fede265fbba7bc7dcb613bd5c12e1126 (MD5) Previous issue date: 2010-05-16 / (Epiphytic algae community of (with emphasis on diatoms) of Palm swamps of Goias State). The present study is the first to evaluating epiphytic algae community structure of in the subsystem Palm swamps in the Cerrado. The general hypotheses of this study were: impacted Palm swamps are under greater influence of allochthonous material, causing changes in limnological characteristics, as the record of increased nutrient levels and turbidity; the structure of ephiphytic algae community is influenced by environmental characteristics, and impacted Palm swamps have diatom as dominant group of epiphyton due to the adaptive cytomorphological characteristics. The overall objective was to analyze the spatial variation of limnological (physical, chemical and biological) and climatological characteristics of 23 Palm swamps in the Goias State under different environmental impacts and to evaluate epiphytic algae community structure of in relation to environmental characteristics of Palm swamps. This dissertation was structured in a general introduction and two chapters in the form of articles: (Article 1) Spatial variation of limnological and climatic characteristics of Palm swamps under different environmental impacts in the Goias State; (Article 2) Relationship between the structure epiphytic algal community (with emphasis on diatoms) and Palm swamps under different environmental impacts in the Goias State. Sampling was conducted in August and September 2008, in the cities of Caldas Novas, Catalan, Cidade de Goiás, Goiânia, Ipameri, Morrinhos and Piracanjuba. Environmental data of Palm swamps were analyzed: morphometric, climatological and limnological characteristics (pH, water temperature, conductivity and turbidity), nutrients (total nitrogen, total phosphorus and silica), chlorophyll-a and the attributes of epiphytic algae community structure (composition, richness, density, biovolume, diversity and evenness). The abiotic data were collected simultaneously to the biotic data. Epiphytic material was obtained from grasses (Poaceae). Environments showed great variation in the values of electric conductivity, turbidity, total nitrogen and epiphytic biomass, low pH and total phosphorus, and high concentrations of silica. Palm swamps groups under different environmental impacts were discriminated mainly by pH and turbidity. Among the environments preserved only 50% showed oligotrophic characteristics for total nitrogen content, a situation caused by contamination by agricultural activities and urban impacts. It was noted that the acidic water was related to the dystrophic soils of these environments, which showed the pH as an important variable in structuring communities. Greater richness, diversity, density and biovolume of epiphytic algae were recorded in Palm swamps impacted. Zignemafíceas were the most representative in species richness followed by diatoms. Palm swamps impacted had greater density and biovolume of epifiton. Eunotia bilunaris (Ehrenberg) Mills was predominant in the Palm swamps with the highest density of epiphytic algae. Tapinothrix bornetii Sauvageau had higher biovolume in the community. Two taxa (Gomphonema sp.2 and Oedogonium sp.4) were indicator species to impacted by agriculture Palm swamps. This study reported great features for development of several taxa of Bacillariophyceae, manly to Eunotia Ehrenberg. The epiphytic community of Palm swamps showed less expressive than Veredas impacted, probably related to characteristics such as low light, given the preservation of vegetation cover of arboreal and low concentrations of nutrients. / (Comunidade de algas epifíticas (com ênfase em diatomáceas) de Veredas do estado de Goiás). O presente estudo constitui o primeiro trabalho que avalia a estrutura de comunidade de algas epifíticas no subsistema Veredas do Bioma Cerrado. As hipóteses gerais deste estudo foram: Veredas impactadas estão sob maior influência de materiais alóctones, acarretando alterações nas caracteristicas limnológicas, como o registro de maiores valores de nutrientes e turbidez; a estrutura da comunidade de algas epifíticas é influenciada pelas características ambientais, sendo que Veredas impactadas apresentam as diatomáceas como grupo dominante do epifíton devido às características adaptativas cito-morfológicas. Os objetivos gerais foram analisar a variação espacial de características limnológicas (físicas, químicas e biológicas), e climatológicas de 23 Veredas localizadas no estado de Goiás sob diferentes impactos ambientais; e avaliar a estrutura de comunidades de algas epifíticas em relação as características ambientais das Veredas. Esta dissertação foi estruturada em introdução geral e dois capítulos em forma de artigos: (Artigo 1) Variação espacial de características limnológicas e climatológicas de Veredas sob diferentes impactos ambientais no estado de Goiás; (Artigo 2) Relação entre a estrutura de comunidade de algas epifíticas (com ênfase em diatomáceas) e Veredas sob diferentes impactos ambientais no Estado de Goiás. A amostragem foi realizada em agosto e setembro de 2008, nas proximidades dos municípios de Caldas Novas, Catalão, Cidade de Goiás, Goiânia, Ipameri, Morrinhos e Piracanjuba. Os dados ambientais analisados foram: características morfométricas, dados climatológicos, variáveis limnológicas (pH, temperatura da água, condutividade elétrica e turbidez), nutrientes (nitrogênio total, fósforo total e sílica), clorofila-a e os principais atributos da estrutura de comunidade de algas epifíticas (composição, riqueza, densidade, biovolume, diversidade e equitabilidade). Os dados abióticos foram coletados simultaneamente aos dados bióticos. O material epifítico foi obtido de gramíneas (Poaceae). Os ambientes apresentaram grande variação nos valores de condutividade elétrica da água, turbidez, nitrogênio total e biomassa epifítica, baixos valores de pH e fósforo total, e altas concentrações de sílica. Os grupos de Veredas sob diferentes tipos de impacto ambiental foram discriminadas principalmente pelas variáveis pH e turbidez. Entre os ambientes conservados, apenas 50% apresentaram características oligotróficas para concentração de nitrogênio total, situação provocada pela possível contaminação por atividades de agropecuária ou impactos urbanos. Notou-se que as águas ácidas foram relacionadas com os solos distróficos desses ambientes, o que evidenciou o pH como variável importante na estruturação das comunidades. Maior riqueza, diversidade, densidade e biovolume de algas epifíticas foram registrados em Veredas impactadas. Zignemafíceas foram as mais representativas em riqueza específica seguida por diatomáceas. Eunotia bilunaris (Ehrenberg) Mills foi predominante ao ambiente com a maior densidade algal. Tapinothrix bornetii Sauvageau apresentou o maior biovolume das comunidades. Dois táxons (Gomphonema sp.2 e Oedogonium sp.4) apresentaram-se como espécies indicadoras à Veredas impactadas por agropecuária. Este estudo registrou características ótimas para o desenvolvimento de vários táxons de Bacillariophyceae, principalmente para o gênero Eunotia Ehrenberg. As Veredas conservadas apresentaram comunidade epifítica menos expressiva que as impactadas, fato provavelmente associado a baixa iluminação das Veredas conservadas, dada à preservação da cobertura vegetal de porte arbóreo e baixas concentrações de nutrientes.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / As algas diatomáceas apresentam-se distribuídas em diversos ambientes aquáticos e respondem rapidamente a mudanças ambientais, por essas razões têm sido usadas como indicadoras de contaminação orgânica e eutrofização. São conhecidas respostas de muitos táxons às mudanças ambientais e tolerância à composição química da água e ao pH, como também à poluição orgânica (saprobidade). Visando aprofundar os estudos sobre as diatomáceas do igarapé Caranã, Boa Vista RR foi desenvolvido o presente estudo, que teve por objetivo avaliar a qualidade da água do igarapé Caranã, utilizando parâmetros físico-químicos e biológicos. No período seco (novembro e dezembro de 2009 e janeiro de 2010) e no chuvoso (abril, maio e junho de 2010), foram feitas amostragens de diatomáceas epífitas em quatro pontos, ao longo do igarapé Caranã, tendo o material sido oxidado e posteriormente, preparadas lâminas permanentes. Simultaneamente, foram determinados o pH e a temperatura da água, como também coleta da água para análises microbiológicas. Foram registrados 90 táxons, em nível específico, divididos em 20 gêneros e 13 famílias. As famílias mais representativas foram a Eunotiaceae e Pinnulariaceae. Eunotia e Pinnularia foram os gêneros mais representativos, com 28 e 14 táxons, respectivamente. Um total de 24 espécies foram consideradas abundantes: Actinella mirabilis (Eulenstein ex Grunow) Grunow, Brachysira rostrata (Krasske) Metzeltin e Lange-Bertalot, Brachysira sp., Encyonema perminutum Krammer, Encyonopsis frequentis Krammer, Eunotia cf. bilunaris (Ehrenberg) Mills, E. incisa Gregory var. incisa, E. luna var. aequalis Hustedt, E. paludosa Grunow aff, paludosa, E. synedraeformis var. angustata Hustedt, E. transfuga, E. yanomami Metzeltin e Lange-Bertalot, Fragillaria javanica Hustedt, Frustulia rhomboide (Ehernberg) De Toni var. rhomboides, F. saxonica Rabenhorst, F. undosa, Frustulia sp., Gomphonema archeavibrio Lange-Bertalot; Reichardt, G. lagenula Kützing, Luticola monita (Hustedt) D.G. Mann, Pinnularia brauniana (Grunow) Mills, P. divergens W. Smith (sensu lato), Stenopterobia delicatissima (Lewis) Van Heurck sensu lato, Surirella linearis var. constricta Grunow. Todas as espécies caracterizadas junto com o pH corroboraram os dados da literatura pesquisada, onde considera-se, portanto, as águas do igarapé Caranã, pela presença e abundância dos gêneros Eunotia e Pinnularia, como tropicais, oligotróficas e ácidas. As espécies encontradas no estudo são citadas pela primeira vez para o Estado de Roraima. / The algae diatoms present were distributed in various aquatic environments and respond quickly to environmental changes, theyhave bee used as indicators of organic pollution and eutrophication. The responses are known of many taxa to environmental changes and tolerance to water chemistry and pH, as well as resistance to organic pollution (saprophytic). In order to deepen the study of diatoms in stream Caranã, Boa Vista RR, this study had as objective to evaluate the quality of water in stream Caranã, using physico-chemical and biological. During the dry season (November and December 2009, and January 2010), and the rainy season (April, May and June 2010) samples were made of epiphytic diatoms were collected at four points along the stream Caranã, where the material was oxidized and, then permanently placed on slides. We determined the pH and water temperature, as well as water collection for microbiological analysis. 90 taxa were recorded, at specific level, divided into 20 genera and 13 families. The most widely represented families were Eunotiaceae and Pinnulariaceae. Eunotia and Pinnularia genera had 28 and 14 taxa, respectively. A total of 24 species were considered abundant: Actinella mirabilis (Eulenstein ex Grunow) Grunow, Brachysira rostrata (Krasske) Lange- Bertalot and Metzeltin, Brachysira sp., Encyonema perminutum Krammer, Encyonopsis Frequentis Krammer, Eunotia cf. bilunaris (Ehrenberg) Mills, E. incisa Gregory var. incisa, E. luna var. aequalis Hustedt, E. paludosa Grunow aff, paludosa, E. synedraeformis var. angustata Hustedt, E. trasfuga, E. yanomami and Lange-Bertalot Metzeltin, Fragillia javanica Hustedt, Frustulia rhomboide (Ehernberg) De Toni var. rhomboide, F. saxonica Rabenhorst, F. undosa, Frustulia sp., Gomphonema archeavibrio Lange-Bertalot; Reichardt, G. lagenula Kützing, Luticola monita (Hustedt) D.G. Mann, Pinnularia brauniana (Grunow) Mills, P. divergens W. Smith (sensu lato), Stenopterobia delicatissima (Lewis) Van Heurck sensu lato, Surirella linearis var. constricta Grunow. All species featured along with the pH data corroborate the literature, where it is considered, therefore, the waters of the stream Caranã, the presence and abundance of Eunotia and Pinnularia, and tropical, oligotrophic and acidic. The species found in the study are first cited in the State of Roraima.

Le but de ce travail a été de réaliser des études téphrostratigraphiques sur des environnements sédimentaires variés dans le but de définir, dans un premier temps, le degré d'efficacité des techniques de détection des téphras classiquement utilisées. Le travail d'analyse des cendres volcaniques a tout d'abord été ciblé sur des téphras clés et anciennement étudiés sur des sites reconnus, en Belgique et dans le Massif du Jura, dans le but d'actualiser des données avec les techniques d'analyses performantes actuelles. Le travail a ensuite été étendu à des sites de l'Est du Massif Central, dont le potentiel téphrostratigraphique n'avait jamais été exploité, offrant ainsi la possibilité de s'assurer sans ambiguïté de la source de cryptotéphras repérés dans le Jura et en Suisse, dont l'origine était incertaine. Ce travail d'échantillonnage a été réalisé dans des milieux lœssiques, carbonatés et tourbeux permettant également de discuter des conditions de conservation des dépôts volcaniques et de leurs constituants. Les études téphro-chrono-stratigraphiques s'inscrivent fréquemment dans une réflexion sur l'impact écologique et environnemental des éruptions volcaniques. Un nombre croissant d'études tendent à montrer un impact écologique des téphras, en étant la cause de bloom de diatomées. Ce travail de thèse a permis de discuter de cet aspect environnemental qui a été mené dans le Jura, dans un environnement défavorable à la préservation des diatomées. / The challenge of this work was to carry out several tephrostratigraphic studies in various sedimentary environments in order to test the efficiency of classical detection methods of tephra layers. First, analysis has been focused on tephra keys, previously studied in known sites, in Belgium and in the Jura Mountains, in order to update data with current analytical techniques. This work was later expanded to sites from eastern French Massif Central, an area with unexploited tephrostratigraphic potential, which offers the possibility to precise the source of cryptotephras identified in the Jura and Switzerland whose origin was uncertain. This work has been carried out in tephras sampled in loess, carbonate maris and peat allowing to discuss conservation conditions of volcanic deposits. Sorne tephro-chrono-stratigraphic studies show ecological and environmental impacts of volcanic deposits in lakes and peatlands, such as diatom blooms. This thesis allows to discuss this environmental aspect in carbonate maris, i.e. an unfavorable environment for preservation of diatoms.

Les diatomées sont une composante majeure des écosystèmes marins et sont caractérisées par une grande diversité. L’objectif général de cette thèse est d’étudier les facteurs de contrôle des diatomées dans la Zone Côtière Belge (ZCB). Pour ce faire, la modélisation par groupes fonctionnels et l’approche basée sur les traits sont combinées :la première fournit un cadre écosystémique utile pour étudier les interactions des diatomées avec les compartiments biotiques et abiotiques de l’écosystème, et la seconde permet de représenter de façon efficace leur diversité fonctionnelle.<p><p>Dans un premier temps, puisque la taille est reconnue comme un trait majeur affectant de nombreux aspects de la valeur sélective du phytoplancton, la dépendance au biovolume de différents traits des diatomées a été établie sur base d’observations disponibles dans la littérature. Cette revue a montré qu’un compromis sépare les diatomées sur base de leur biovolume :les petites espèces sont meilleures compétitrices pour l’acquisition des ressources mais plus sensibles au broutage, et inversement. <p>Sur cette base, un ré-analyse d’un jeu de données incluant des comptages et mesures de biométrie avec l’identification de 68 taxons dans la ZCB entre 1992 et 2000 a été réalisée, avec une attention particulière pour la structure en termes de taille de la communauté de diatomées. Un regroupement des diatomées en fonction de leur biovolume a été réalisé sur base de leur évolution saisonnière typique. L’analyse de leur évolution temporelle suggère que la communauté des diatomées est composée d’assemblages avec une évolution saisonnière et interannuelle distinctes qui répondent vraisemblablement différemment aux conditions environnementales.<p>Afin d’étudier plus en profondeur les facteurs environnementaux contrôlant la structure en termes de taille de la communauté des diatomées dans la ZCB, le module diatomées du modèle MIRO, qui représente l’écosystème planctonique de la ZCP, a été modifié afin d’inclure les dépendances à la taille de quatre traits des diatomées. Cet outil reproduit correctement l’évolution saisonnière du biovolume moyen de la communauté, qui est caractérisé par de plus petites diatomées au printemps qui maximisent l’acquisition de ressources tandis que la prévalence du broutage en été induit une transition vers des espèces plus grandes. Le modèle a également été exploité pour étudier la gamme de tailles viables dans la ZCB en fonction des conditions environnementales. <p>Les résultats du modèle basés sur les traits ont ensuite été analysés sur la période 1992-2000. Les simulations ont mis en évidence les interactions complexes entre les processus physiques, de contrôles par les ressources et par le broutage, qui sont susceptibles de déterminer la variabilité interannuelle de la structure en termes de taille des diatomées dans la ZCB. La comparaison de ce modèle adaptatif avec un modèle plus conventionnel qui ne représente pas de diversité interne aux diatomées suggère que le premier produit une réponse légèrement plus flexible que le dernier, mais que la rigidité de la réponse simulée demeure un problème avec le modèle adaptatif qui reste incapable de représenter des évènements extrêmes de biomasse ou de structure de la communauté. Cela suggère que des développements supplémentaires du modèle sont nécessaires, en particulier du module zooplancton.<p>Finalement, une fonction écologique particulière est abordée dans une dernière section de cette thèse :la production d’une neurotoxine par certaines diatomées du genre Pseudo-nitzschia. Cette fonction a été incluse comme un métabolisme secondaire dans un modèle idéalisé de la croissance de Pseudo-nitzschia afin d’étudier les facteurs contrôlant la production de la toxine. Il est notamment montré que l’environnement lumineux est déterminant lorsque les conditions menant à la production de toxine sont rencontrées. <p><p>/<p><p>Diatoms are a key component of marine ecosystems and are characterized by an important diversity. The general objective of this thesis is to investigate the bottom-up and top-down controls of diatoms in the Belgian Coastal Zone (BCZ). This is done through the integration of their functional diversity into a coherent framework. In order to achieve this, Plankton Functional Type modelling and trait-based approaches are combined: the former provides an ecosystem context convenient to study the interactions of diatoms with biotic and abiotic compartments, and the latter allows an efficient representation of their functional diversity. <p><p>As a first step, since size is recognized as a master trait shaping many aspects of phytoplankton fitness, the cell volume dependences of diatom functional traits were compiled from observations available in the literature. This review showed that a trade-off distinguishes diatoms on the basis of their cell volume: smaller species are better competitor for resource acquisition but sensitive to grazing, and inversely. <p>On this basis, a re-analysis of a dataset including diatom cell counts and biometry with the identification of 68 taxa in the BCZ over the 1992-2000 period was carried out, with a focus on the size structure of the diatom community. A clustering of diatoms according to their cell volume was realized on the basis of their average seasonality. Investigation of their time evolution suggested that the diatom community in the area is composed of assemblages with distinct seasonal and interannual evolution that likely respond differently to environmental conditions.<p>In order to further investigate the bottom-up and top-down constrains on the size structure of the diatom community in the BCZ, the diatom module of the MIRO model, which represents the planktonic ecosystem of the BCZ, was modified in order to accommodate size-dependences of four diatom functional traits. This tool adequately reproduced the seasonal evolution of the mean cell volume of the diatom community, which is characterized by smaller diatoms in spring that maximize resource acquisition while the prevalence of grazing pressures in summer induces a shift towards larger species. The model was also used to investigate the range of viable diatom sizes in response to the bottom-up and top-down pressures in the BCZ.<p>Results of the trait-based adaptive model were then analysed over the 1992-2000 period. Simulations evidenced the complex interactions between physical, bottom-up and top-down processes that are likely to govern the interannual variability in the size structure of diatom in the area. Comparison of the adaptive model with a more conventional model resolving no diversity within diatoms suggested that the former produces a slightly more flexible response than the latter, but showed that the rigidity of the simulated response persists with the adaptive model which remains unable to catch extreme biomass and community structure events. This calls for further developments of other compartments of the model, more particularly zooplankton.<p>Finally, a peculiar ecological function is addressed on its own in the last section of this thesis: the toxigenicity of some species of the genus Pseudo-nitzschia. This function was added as a secondary metabolism in an idealized model of Pseudo-nitzschia growth in order to investigate the factors affecting toxin production. It notably showed that light was determinant under conditions leading to its production.<p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Depuis la découverte de Phaeodactylum tricornutum par Bohlin en 1897, sa classification au sein de l'arbre de la vie a été controversée. En utilisant des morphotypes ovales et fusiformes Lewin a décrit en 1958 plusieurs traits caractéristiques de cette espèce rappelant la structure des diatomées mettant ainsi fin à la controverse sur la classification de P. tricornutum au sein des Bacillariophycées. Pour se faire, trois morphotypes (ovale, fusiforme et triradié) de Phaeodactylum tricornutum ont été observés. Au cours d’une centaine d’années environ, de 1908 à 2000, 10 souches de Phaeodactylum tricornutum (appelées écotypes) ont été collectées et stockées soit de manière axénique ou en l’état avec leur populations naturelles de bactéries dans les centres des ressources génétiques pour algues, cryo-préservées quand cela est possible. Divers outils cellulaires et moléculaires ont été établis pour disséquer et comprendre la physiologie et l'évolution de P. tricornutum, et/ou les diatomées en général. Grâce à des décennies de recherche et les efforts déployés par de nombreux laboratoires que P. tricornutum est aujourd’hui considérée comme une espèce modèle des diatomées. Le sujet de ma thèse traite majoritairement de la composition génétique et épigénétique du génome de P. tricornutum ainsi que de la diversité morphologique et physiologique sousjacente au sein des populations naturelles prospectées à différents endroits du globe. Pour se faire, j’ai généré les profils chromatiniens en utilisant différentes marques des modifications post-traductionnelles des histones (chapitres 1 et 2) et a également comparé la variation naturelle dans la distribution de certaines marques clés entre deux populations d’écotypes (chapitre 4). Nous avons également généré une carte de la diversité génétique à l’échelle du génome chez 10 écotypes de P. tricornutum révélant ainsi la présence d'un complexe d'espèces dans le genre Phaeodactylum comme la conséquence d’une hybridation ancienne (chapitre 3). Sur la base de nombreux rapports antérieurs et des observations similaires au sein de P. tricornutum, nous proposons l’hybridation naturelle comme une base solide et une possibilité plausible pour expliquer la diversité des espèces chez lest diatomées. De plus, nous avons mis à jour les annotations fonctionnelles et structurelles du génome de P. tricornutum (Phatr3, chapitre 2) et mis au point un algorithme de logiciel convivial pour aller chercher les cibles CRISPR du système d’édition du génome CRISPR / cas9 chez 13 génomes de phytoplancton incluant P. tricornutum (chapitre 5). Pour accomplir tout cela, j'ai utilisé diverses méthodes à la pointe de l’état de l’art comme la spectrométrie de masse, l’immunoprécipitation de la chromatine suivie de séquençage à haut débit ainsi que les séquençages du génome entier, de l'ARN et des protocoles d'édition du génome CRISPR et plusieurs logiciels / pipelines de calcul. Ainsi, le travail de thèse fournit une plate-forme complète qui pourra être utilisée à l’avenir pour des études épigénétiques, de génétiques moléculaires et fonctionnelles chez les diatomées en utilisant comme espèce modèle Phaeodactylum tricornutum. Ce travail est pionnier et représente une valeur ajoutée importante dans le domaine de la recherche sur les diatomées en répondant à des questions nouvelles ouvrant ainsi de nouveaux horizons à la recherche en particulier en épigénétique qui joue un rôle important mais pas encore assez apprécié dans le succès écologique des diatomées dans les océans actuels. / Since the discovery of Phaeodactylum tricornutum by Bohlin in 1897, its classification within the tree of life has been controversial. It was in 1958 when Lewin, using oval and fusiform morphotypes, described multiple characteristic features of this species that resemble diatoms structure, the debate to whether classify P. tricornutum as a member of Bacillariophyceae was ended. To this point three morphotypes (oval, fusiform and triradiate) of Phaeodactylum tricornutum have been observed. Over the course of approximately 100 years, from 1908 till 2000, 10 strains of Phaeodactylum tricornutum (referred to asecotypes) have been collected and stored axenically as cryopreserved stocks at various stock centers. Various cellular and molecular tools have been established to dissect and understand the physiology and evolution of P. tricornutum, and/or diatoms in general. It is because of decades of research and efforts by many laboratories that now P. tricornutum is considered to be a model diatom species. My thesis majorly focuses in understanding the genetic and epigenetic makeup of P. tricornutum genome to decipher the underlying morphological and physiological diversity within different ecotype populations. To do so, I established the epigenetic landscape within P. tricornutum genome using various histone post-translational modification marks (chapter 1 and chapter 2) and also compared the natural variation in the distribution of some key histone PTMs between two ecotype populations (chapter 4). We also generated a genome-wide genetic diversity map across 10 ecotypes of P. tricornutum revealing the presence of a species-complex within the genus Phaeodactylum as aconsequence of ancient hybridization (Chapter 3). Based on the evidences from many previous reports and similar observations within P. tricornutum, we propose natural hybridization as a strong and potential foundation for explaining unprecedented species diversity within the diatom clade. Moreover, we updated the functional and structural annotations of P. tricornutum genome (Phatr3, chapter 2) and developed a user-friendly software algorithm to fetch CRISPR/Cas9 targets, which is a basis to perform knockout studies using CRISPR/Cas9 genome editing protocol, in 13 phytoplankton genomes including P. tricornutum (chapter 5). To accomplish all this, I used various state-of-the-art technologies like Mass-Spectrometry, ChIPsequencing, Whole genome sequencing, RNA sequencing, CRISPR genome editing protocols and several computational softwares/pipelines. In brief, the thesis work provides a comprehensive platform for future epigenetic, genetic and functional molecular studies in diatoms using Phaeodactylum tricornutum as a model. The work is an addon value to the current state of diatom research by answering questions that have never been asked before and opens a completely new horizon and demand of epigenetics research that underlie the ecological success of diatoms in modern-day ocean.