M.Sc. / Water resources in South Africa are scarce and need to be protected and managed in a sustainable way for future generations. Food supply is a great priority worldwide and the pressure to produce enough food has resulted in the expansion of irrigation and the steadily increasing use of fertilizers and pesticides to achieve higher yields. Rivers are impacted by agriculture through increased suspended sediment loads (which affects primary production, habitat reduction and introduction of absorbed pollutants), elevated nutrient inputs (which may increase the abundances of algae and aquatic plants), salinization and pesticide runoff (which eliminates species intolerant to these conditions and therefore impacts on the normal production of the river system). Aquatic biota plays an integral part in the functioning of aquatic ecosystems. Biological monitoring is used to assess ecosystem health and integrity. Biological communities reflect the overall integrity of the river ecosystem by integrating various stressors and therefore provide a broad measure of their synergistic effects. The research area falls within the Lower Vaal Water Management Area (WMA), which lies in the North-West and Northern Cape Provinces. The lower Vaal River and the Harts River (one of the tributaries of the Vaal) are the river systems under investigation in this study. Farming activities ranges from extensive livestock production and rain fed cultivation to intensive irrigation enterprises at Vaalharts (such as maize, cotton and groundnuts). The Vaalharts is the largest irrigation scheme in South Africa. Salinity is of concern in the lower reaches of the Harts- and Vaal Rivers, due to saline leachate from the Vaalharts irrigation scheme. Agricultural inputs are known to affect aquatic communities and chemicals (e.g. pesticides, herbicides, fertilizers) are extensively used in the Vaalharts irrigation scheme. At present there are no data on the effect of these chemicals on the aquatic biota of the lower Harts- and Vaal Rivers. The aims of this study were to assess the diatom- and macroinvertebrate community structures, ecosystem integrity and macroinvertebrate feeding traits (functional feeding groups – FFGs) in relation to land use.

Dans cette thèse, deux axes ont été investigués. Le premier visait à étudier les relations Si-Corg et plus précisément Si-Clipides. La mise au point d’un protocole destiné à l’analyse des lipides associés aux frustules a été réalisée. Ce protocole nous a permis de montrer que ces lipides, représentant environ 1 % du Corg total, étaient dominés par des acides gras saturés (14:0, 16:0 et 18:0) chez Thalassiosira weissflogii. Le suivi de cette fraction au cours d’expériences de dégradation nous a permis de confirmer l’hypothèse de protection de la matière organique (MO) par la silice biogénique. Ces relations Si-Corg ont également été analysées après une croissance carencée en nitrate. Les résultats montrent que cette fraction n’était pas affectée par une carence en nitrate chez T. weissflogii.Notre deuxième axe d’investigation a consisté à étudier l’impact des conditions nutritives de croissance (carence en N, P et Si) sur la composition biochimique de T. weissflogii et sur sa biodégradation. Le calcul des constantes de dégradation de ses différents pools constitutifs (COP, NOP, monosaccharides et lipides) nous a permis de juger de l’efficacité des diatomées carencées, à exporter du Corg. La dégradation du Corg est peu affectée par ces carences à l’échelle globale mais sa quantité absolue par cellule augmente. De plus, la réponse physiologique de nos cellules face à une carence en Si semble être découplée du métabolisme énergétique contrairement aux réponses observées face aux carences en N et P. Cette variabilité de la réponse physiologique pourrait expliquer en partie la variabilité interbassins observée dans les corrélations entre flux de Si et de Corg en profondeur. / In this thesis, two axes of investigation on the diatom Thalassiosira weissflogii have been studied. The first one aimed to study Si-OC relationships and more specifically Si-OClipids. The development of an adapted protocol designed to analyse lipids intimately associated with frustules has been carried out. This protocol enabled us to show that lipids, amounting to about 1 % of the total OC, were dominated by saturated fatty acids (14:0, 16:0 and 18:0) in T. weissflogii cells. The monitoring of this fraction during degradation experiments enabled us to confirm the protective role of biogenic silica on organic matter (OM). These Si-OC relationships have also been analyzed after diatoms grew in nitrate starved conditions. Results indicated that this fraction was not impacted by nitrate starvation in T. weissflogii.Our second axis of investigation was to study the impact of nutrient growth conditions (starvations in N, P and Si) on T. weissflogii biochemical composition and its biodegradation. The estimation of degradation rate constants for some OM pools (POC, PON, monosaccharides and lipids) enabled us to assess the OM quality changes and the efficiency of nutrient starved diatoms to export OC. Interestingly, the degradation of OC is weakly affected by these starvations at the global scale (POC) but its absolute amount per cell increases. Moreover, the physiological response of cells facing Si starvation seems to be uncoupled with energetic metabolism, the opposite of observed responses during N and P starvations. This variability of the physiological response could explain partly the inter basin variability observed in Si and OC flux in depth.

Visual assessment of discontinuities in the morphological features of diatom cells has been widely used in the discovery and delimitation of diatom species. However, a multidisciplinary approach to species-level taxonomy has revealed hidden diversity within the traditional diatom morphospecies. Consequently, this work examined both the natural and clonal populations of diatoms by diverse traditional and modern approaches, in order to assess the diversity, ecology, and distribution of diatom species. Although a detailed investigation of natural diatom samples was confounded by uncertain morphological boundaries between the traditional diatom species, it recognized that the diversity was relatively high; even one new diatom species was described using the morphological species concept. The multivariate statistical analyses showed that the variation of natural communities of traditional diatom morphospecies reflected differences in the local environmental conditions, as well as microhabitat heterogenity within a region. Since each diatom morphospecies is most likely a complex of sibling species, the two model traditional morphospecies were investigated, in order to assess morphological variation, genetic diversity, and/or the reproductive compatibility of monoclonal cultures. Even though isolated...

The occurrence of some diatoms depends on degree of pollution and water quality. Due to this attribute are diatoms used as indicators for the environmental bioassessment. But the maximum use of diatoms for this purpose is complicated by high number of species which are defined based on the ultrastructural morphological features which are indistinguishable without the electron microscope. The aims of this study were to find out the influence of environmental factors, types of habitat and geography on the structure of diatom community. And find out if richness of higher taxonomic levels is correlated with species richness, in this case if it responds with the genetic diversity within diatom species complex Frustulia crassinervia-saxonica. In this study, 49 permanent slides from natural samples were analyzed. Samples were taken from benthos of different types of freshwater habitat - lakes, dams, pools, peat bogs, stream, wet wall on diverse localities in Europe, Canada, Greenland, Chile and New Zealand. In all slides were counted 300 cells which were determined based on the morphological features on genera level. Altogether 43 benthic genera were identified. The results of this thesis showed that number of genera correlated with pH gradient but do not correlate with other environmental factors -...

A associação simbiótica entre a diatomácea cêntrica Chaetoceros coarctatus e o ciliado peritríquio Vorticella oceanica é amplamente conhecida e registrada em diversos estudos, porém nunca havia sido analisada sob o ponto de vista de suas implicações para o movimento destes organismos. A fim de contribuir com novos dados acerca desta associação simbiótica, o presente trabalho analisou a relevância ecológica da simbiose entre Chaetoceros e Vorticella, por meio de um estudo comportamental do deslocamento destes organismos na coluna de água. As associações foram coletadas em águas costeiras de Ubatuba, São Paulo, onde sua ocorrência foi observada em elevada abundância, particularmente durante o verão. Utilizando técnicas de imagem de alta frequência em um sistema óptico tridimensional foi possível descrever os padrões de deslocamento desta associação e avaliar as implicações ecológicas deste comportamento. De acordo com as análises realizadas neste trabalho, pode-se sugerir que o comportamento de deslocamento realizado pela associação Chaetoceros-Vorticella na coluna de água resulta em vantagens tanto para o epibionte quanto para o hospedeiro. Em termos de submesoescala, este estudo sugere que o deslocamento realizado pela associação Chaetoceros-Vorticella pode contribuir para a formação de camadas finas, levando à formação de hotspots de atividade biogeoquímica e interações tróficas no ecossistema pelágico. / The symbiotic association between the centric diatom Chaetoceros coarctatus and the peritrich ciliate Vorticella oceanica is widely known and reported in several studies, but its implications for the movement of these organisms have never been analyzed. In order to contribute with new data about this symbiotic association, the present study investigated the ecological relevance of the Chaetoceros-Vorticella association by recording displacement parameters of these organisms in the water column. The associations were collected in coastal waters of Ubatuba, São Paulo, where their occurrence was observed in high abundance, particularly during the summer. Using high-resolution imaging techniques in a three dimensional optical system it was possible to describe the displacement patterns of this association and to provide initial insights about the ecological implications of this behavior. It is suggested that the displacement behavior performed by the Chaetoceros-Vorticella association in the water column is beneficial for both the epibiont and the host. In terms of submesoscale processes, this study indicates that the displacement carried out by the Chaetoceros-Vorticella association may contribute to the formation of thin layers, leading to the formation of hotspots of biogeochemical activity and trophic interactions in the pelagic ecosystem.

Lake sediment cores spanning the last 2000 years from four sites across the Canadian Arctic Archipelago (CAA) document the responses of terrestrial and freshwater ecosystems to regional climate variability. Biogenic silica (BSi) records in cores from Banks Island, NWT (Lake B503; 72.3245, -123.4036, 84 masl), Bathurst Island, Nunavut (PR01; 75.6497, -99.1144, 30 masl), Prince of Wales Island, Nunavut (SW08; 72.3177, -97.2678, 104 masl), and Ellesmere Island, Nunavut (CV03; 79.9211, -82.9348, 363 masl) were used to examine the relationship between diatom production and climate. A pollen record from Prince of Wales Island provided the first high-resolution July temperature reconstruction for the last 1000 years for the central CAA. Dissolution was evident in three out of the four lakes; core SW08 contained no BSi above detection and cores CV03 and PR01 only contained values above detection in the uppermost sediments, suggesting that the preservation of biogenic silica (BSi) in the sediment is likely influenced by sedimentary carbonates. A BSi sequence from core B503 showed that diatom production was affected by climate changes such as the Medieval Climate Anomaly and the Little Ice Age. The vegetation on southern Prince of Wales Island underwent marked transitions during the Little Ice Age and Medieval Climate Anomaly, which was mainly observed in the proportion of Cyperaceae and Poaceae. The mean July temperature reconstruction showed a long-term cooling from 1080-1915 CE with a sustained cold period from 1800-1915 CE prior to 20th-century warming. A synthesis of paleoclimate records from across the Arctic demonstrated that pollen-based reconstructions record both high and low frequency climate variability, when sampling resolution is sufficient, and can improve regional climate reconstructions.

A associação simbiótica entre a diatomácea cêntrica Chaetoceros coarctatus e o ciliado peritríquio Vorticella oceanica é amplamente conhecida e registrada em diversos estudos, porém nunca havia sido analisada sob o ponto de vista de suas implicações para o movimento destes organismos. A fim de contribuir com novos dados acerca desta associação simbiótica, o presente trabalho analisou a relevância ecológica da simbiose entre Chaetoceros e Vorticella, por meio de um estudo comportamental do deslocamento destes organismos na coluna de água. As associações foram coletadas em águas costeiras de Ubatuba, São Paulo, onde sua ocorrência foi observada em elevada abundância, particularmente durante o verão. Utilizando técnicas de imagem de alta frequência em um sistema óptico tridimensional foi possível descrever os padrões de deslocamento desta associação e avaliar as implicações ecológicas deste comportamento. De acordo com as análises realizadas neste trabalho, pode-se sugerir que o comportamento de deslocamento realizado pela associação Chaetoceros-Vorticella na coluna de água resulta em vantagens tanto para o epibionte quanto para o hospedeiro. Em termos de submesoescala, este estudo sugere que o deslocamento realizado pela associação Chaetoceros-Vorticella pode contribuir para a formação de camadas finas, levando à formação de hotspots de atividade biogeoquímica e interações tróficas no ecossistema pelágico. / The symbiotic association between the centric diatom Chaetoceros coarctatus and the peritrich ciliate Vorticella oceanica is widely known and reported in several studies, but its implications for the movement of these organisms have never been analyzed. In order to contribute with new data about this symbiotic association, the present study investigated the ecological relevance of the Chaetoceros-Vorticella association by recording displacement parameters of these organisms in the water column. The associations were collected in coastal waters of Ubatuba, São Paulo, where their occurrence was observed in high abundance, particularly during the summer. Using high-resolution imaging techniques in a three dimensional optical system it was possible to describe the displacement patterns of this association and to provide initial insights about the ecological implications of this behavior. It is suggested that the displacement behavior performed by the Chaetoceros-Vorticella association in the water column is beneficial for both the epibiont and the host. In terms of submesoscale processes, this study indicates that the displacement carried out by the Chaetoceros-Vorticella association may contribute to the formation of thin layers, leading to the formation of hotspots of biogeochemical activity and trophic interactions in the pelagic ecosystem.

A biodiversidade e a estrutura da comunidade fitoplanctônica na Zona Costeira Amazônica Brasileira foi avaliada com base em 272 publicações, relativas ao período entre 1861 e 2016, e a partir de oito cruzeiros oceanográficos realizados em diferentes fases do ciclo do Rio Amazonas entre os anos de 2013 a 2015. A seleção das publicações restringiu-se as que apresentaram identificação taxonômica, em diferentes níveis, e/ou quantificação, expressa em densidade celular, obtidas exclusivamente através de microscopia ótica. A composição específica e a densidade celular do fitoplâncton foram avaliadas através da metodologia Utermöhl (1958). As informações disponíveis, principalmente sob a forma de resumos em congressos (67%), monografias (13%) e artigos publicados em periódicos (11%), foram resgatadas de estudos desenvolvidos no litoral dos Estados do Pará (131), Maranhão (105) e Amapá (3), assim como na plataforma continental (36). Entre os ecossistemas mais bem estudados, estão os estuários (135 referências), plataforma continental (36 referências) e as praias (30), sendo o enfoque ecológico o principal objetivo das investigações científicas (96%). Atualmente, o inventário de espécies inclui 1157 táxons distribuídos em 612 diatomáceas, 252 dinoflagelados, 199 clorofíceas, 56 cianobactérias, 19 cocolitoforídeos, 19 euglenofíceas e uma criptofícea. Com base nesta revisão e nas amostragens realizadas neste estudo, a análise da estrutura da comunidade fitoplanctônica na Plataforma Continental Amazônica é característica de ambientes costeiros sob influência de plumas fluviais, com dois cenários ecológicos relacionados aos períodos de vazão do Rio Amazonas: um de maior influência, nos meses de abril e julho, e outro oposto, nos meses de outubro e janeiro. Observou-se uma distribuição em faixas, de acordo com as características ambientais e a estrutura da comunidade fitoplanctônica, divididas em plataforma interna sob influência da pluma, zona de transição e plataforma externa com influência oceânica. As Diatomáceas são responsáveis pelas altas densidades (105 cel.L-1) na região costeira, especialmente sob influência da pluma, contribuindo para o incremento de Clorofila a (>10 &mu;g.L-1). Na porção oceânica, sem influência da pluma, as concentrações de Cla são baixas (<2 &mu;g.L-1) e predominam (104 cel.L-1) as cianobactérias filamentosas e cocolitoforídeos. A variabilidade temporal da descarga do Rio Amazonas e, consequentemente, da dinâmica espacial da pluma, é o principal fator responsável por mudanças na salinidade e disponibilidade de nutrientes, determinando a estrutura da comunidade fitoplanctônica. Este estudo reforça a importância da manutenção de séries temporais e o levantamento da biodiversidade para a compreensão da dinâmica da comunidade fitoplanctônica em ambientes de alta complexidade, como a Plataforma Continental Amazônica. / Phytoplankton biodiversity and structure in the Brazilian Amazon Coastal Zone was evaluated based on 272 publications from the period between 1861 and 2016 and from eight oceanographic cruises carried out in different phases of the Amazon river hydrograph between the years 2013 to 2015. Selected publications were restricted to those which presented taxonomic identification at different levels, and / or quantification in terms of cell density, obtained exclusively by optical microscopy. Specific composition and phytoplankton cell density was evaluated by Utermöhl methodology (1958). Available information in the form of conference abstracts (67%), monographs (13%) and journal articles (11%) were rescued from studies developed on the coast of Pará (131), Maranhão (105) and Amapá (3), as well as on the continental shelf (36). Within these, the best studied ecosystems are estuaries (135 references), the continental shelf (36 references) and the beaches (30), with an ecological approach as the main research objective (96%). Currently, species inventories include 1157 taxa, distributed in 612 diatoms, 252 dinoflagellates, 199 chlorophytes, 56 cyanobacteria, 19 coccolithophorids, 19 euglenoids and one criptoficean. Based on this review and on the results obtained in this study, the structure of the phytoplankton community in the Amazon Continental Shelf is characteristic of coastal environments under the influence of river plumes, with two ecological scenarios related to the Amazon river discharge, one with greater influence in April and July and another with less influence in October and January. The distribution occurs in bands, according to the environmental characteristics and the structure of the phytoplankton community, divided into internal continental shelf under the influence of the plume, transition zone, and external continental shelf with oceanic influence. Diatoms are responsible for the high densities (105 cells.L-1) in the coastal region, especially under the influence of the plume, contributing with the increase of chlorophyll a (> 10 &mu;g.L-1). At the oceanic portion without influence of the plume, Cla concentrations are low (<2 &mu;g.L-1) and filamentous cyanobacteria (104 cells.L-1) and coccolithophorids dominate. The temporal variability of the discharge of the Amazon river and, consequently, the spatial dynamics of the plume, is the main factor responsible for changes in salinity and nutrient availability, determining the structure of the phytoplankton community. This study reinforces the importance of maintaining time series and biodiversity surveys to understand phytoplankton community dynamics in highly complex environments such as the Continental Amazon Shelf.

On considère généralement les biofilms comme des indicateurs biologiques d’alerte, les organismes les composant ayant des temps de génération relativement courts et présentant une grande diversité de preferenda environnementaux et de sensibilité aux altérations anthropiques. Dans ces travaux, les effets de pesticides sur les biofilms de rivière ont été étudiés à différentes échelles de représentativité, allant de mélanges complexes à faible dose en utilisant des extraits d’échantillonneur passif POCIS (Polar Organic Chemical Integrative Sampler) à des molécules testées seules, en passant par des mélanges simples.L’exposition chronique et à faible dose aux extraits de POCIS a révélé des impacts au niveau de la croissance, de la structure (assemblages de diatomées) et du fonctionnement du biofilm en lien avec son exposition passée. De plus les expériences utilisant des molécules testées seules (pesticides et métabolites) et les mélanges simples ont permis de caractériser la toxicité relative des composés présents dans les extraits de POCIS en lien avec leur mode d’action et d’explorer la réponse de descripteurs encore peu utilisés en écotoxicologie comme la construction de Rapid Light Curves (RLCs).Ce travail confirme la pertinence de l’utilisation des extraits d’échantillonneurs passifs comme le POCIS pour mieux appréhender les effets des pesticides en mélanges sur le biofilm de rivière ainsi que l’intérêt des RLCs en tant que descripteur précoces d’exposition aux pesticides. / Biofilms can be regarded as biological warming systems, because they are generally composed of short generation time organisms presenting a large range of environmental preferenda and various sensibilities to anthropogenic disturbance. In the present study, effects of pesticides on river biofilms have been studied at different levels of representativeness, from complex mixtures at low dose represented by POCIS passive sampler extracts (Polar Organic Chemical Integrative Sampler) to molecules tested alone via simple mixtures.Chronic exposure to low dose of POCIS extracts revealed impacts on growth related, structural (diatom assemblages) and functional parameters related to biofilm exposure history. Moreover experiment using single molecules and simple mixtures allowed to characterised the relative toxicity of compounds present in the POCIS extracts in link with their specific mode of action and explore the response of descriptor not very used in ecotoxicology field like the construction of Rapid Light Curves (RLCs).This work confirms the relevance of the use of passive sampler extracts as POCIS in order to better understand the effects of pesticides in mixture on river biofilms as well as the interest of RLCs as early exposure descriptors of pesticides exposure.

Les diatomées sont des algues microscopiques qui contribuent à hauteur de 25% environ à la production primaire planétaire. Les diatomées sont très souvent entourées d’une flore bactérienne, avec laquelle de nombreuses interactions ont été documentées. Les génomes de diatomées contiennent par ailleurs de nombreux gènes dont l’origine prédite est bactérienne.Nous avons étudié Asterionella formosa, une diatomée pennée présente dans de nombreux lacs et cours d’eau à l'aide de données omiques. L’utilisation de la métagénomique a permis de reconstruire 30 génomes bactériens, utilisés pour prédire d'éventuelles interactions avec la diatomée. Le séquençage de la sous-unité 16S de l’ARN ribosomique a montré que les différentes espèces bactériennes avaient une abondance variable au cours des phases de croissance de la diatomée, et que certaines étaient plus souvent au contact de la diatomée que libres dans le milieu. Le génome d'A. formosa a ensuite été séquencé à l'aide de la technologie Pacbio et comparé à ceux d'espèces proches. Enfin, l’impact des bactéries sur les diatomées a été abordé sous l’angle de l’évolution et des transferts horizontaux de gènes, qui ont été prédits à partir des données transcriptomiques d’une centaine de diatomées marines.Ce travail représente une première étape dans l'étude de la communauté bactérienne associée à A. formosa. Des expériences complémentaires incluant l’utilisation de transcriptomique ou métabolomique sont maintenant envisageables. Les données collectées et/ou analysées dans ce travail contribuent d'ores et déjà à l’effort global de caractérisation génomique des diatomées. / Diatoms are ubiquitous microalgae that contribute approximately 25% to the primary production worldwide. Many interactions, either positive, neutral or negative, have been documented between diatoms and bacteria. Diatom genomes also harbor numerous genes of putative bacterial origin.We are studying Asterionella formosa, a freshwater pennate diatom. We characterized the community using a combination of omics and laboratory techniques. We reconstructed of the genome of the diatom as well as 30 individual genomes from co-cultured bacterial species and investigated metabolisms that could support diatom-bacteria interactions. 16S rRNA sequencing revealed that the abundance of some bacterial species was highly variable over the course of A. formosa growth. Some species seemed preferentially attached to the diatom while others were mainly free-living. Then, the reference sequence of the A. formosa genome was improved by additional long-read (Pacbio) sequencing. Last, relationships between diatoms and bacteria were investigated at a broader evolutionary scale, by looking at horizontal gene transfers using transcriptomic data of a hundred marine diatoms.This work is a first step in the study of the dynamic and complex bacterial community associated with the diatom A. formosa. The accurate identification and the reconstruction of the genome of these bacteria will enable further in silico predictions based on metabolic networks and new omics experiments using transcriptomic or metabolomic. This work already contributes to a global effort to study diatoms by the means of genomics.