The interest around hemp is currently renewed for the production of bio-based and renewable materials in the context of global warming. This fibre crop is able to produce large amounts of fibres with different features and industrial application. The most valuable fibres, found in the phloem tissue, are rich in cellulose while relatively poor in lignin, by contrast with the xylem tissue. This thesis aims at studying the events related to the biogenesis of these two types of fibre. Using two different systems, we will investigate the molecular mechanisms related toelongation, secondary growth, deposition and maturation of the cell wall and bast fibre development.Our first objective is to provide a comprehensive overview of the transcriptional factors and phytohormones involved in primary and secondary growth. To this end, the development of the hemp hypocotyl is investigated by a high throughput transcriptomic approach, in addition to proteomics, phytohormone and lignin analyses and microscopy. We show that elongation and secondary growth are characterised by specific patterns of gene expression. The consequences on the biogenesis and modification of the cell walls are widely discussed.The second objective is to decipher the molecular actors associated with the development of the bast fibres. We first show that the contrasting composition of xylem and bast fibres is regulated at the transcriptional level. Next, we highlight the evolution of the transcriptome during the development of the bast fibres, from intrusive growth to thickening. We put a special emphasis on the study of cell wall-related genes (cellulose synthase, fasciclin-like arabinogalactan, transcription factors) and phytohormones. We also formulate several hypotheses to explain the hypolignification of the bast fibres.Finally, this thesis ends with the perspectives raised by our results, notably concerning the deposition of cellulose, non-cellulosic polysaccharides and lignin in the bast fibres. / info:eu-repo/semantics/nonPublished

Modifying root architecture is a strategy that aims to develop plants, which capture nutrients more efficiently and thus suitable for sustainable agriculture with fewer fertilizer inputs. The focus is on nitrate, since it is a major nutritional determinant of root morphology and because of its importance in determining yield. Low concentrations of nitrate in soil stimulate the development of lateral roots, thereby increasing the root surface available for the uptake. Conversely, uniformly concentrations of nitrate inhibit the elongation of lateral roots. The aim of the thesis was to study the natural variation of the root morphological responses to nitrate in Arabidopsis thaliana. First, the manuscript starts with the screening of a core collection of twenty-four accessions, which maximize the genetic diversity within the species, on agar medium at low and moderate nitrate levels. Our results showed that the variability for production and allocation of biomass and root architecture traits exists within the species. Second a detailed characterization is done with eleven accessions showing contrasting root morphological responses to nitrate supply. We demonstrated that at an early development stage, the nitrate uptake efficiency is not implicitly correlated with root system architecture. Third, the genetic determinism of the natural variation of the root system architecture is studied. A combination of genome-wide association mapping on a larger number of accessions (> 300), a linkage mapping with existing recombinant inbred lines and a bulk segregant analysis was carried in order to identify candidate genes involved in root morphological responses to nitrate. The perspectives of this work would be, through a model species to crop pipeline, to translate knowledge from Arabidopsis to Brassica crops that would have a root architecture redesigned to increase the acquisition of nutrients. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Disturbance can take various forms and are characteristic of any ecosystem including mangroves. When maintained within certain allowable limits, disturbances permits maintenance of a given stable state which is equivalent to resilience hence the ecological status is not compromised. Disturbances may disrupt the natural balance of processes within such ecosystems including changes in sediment budgets and salinity and tidal regimes. As such, it may trigger a series of responses in tree establishment and development. While such responses may be displayed in loss of stability of a forest and may culminate in irreversible degradation of the system, disturbances could also result in improved performance of physiological processes and consequently tree growth. It may equally lead to the development of adaptive mechanisms to counteract the resultant otherwise stressful effects. Sediment accretion is one of the important natural processes within the mangrove environment particularly in the face of relative sea level rise. In each case, sediment fluxes are gradual and while the trees thrive from the benefits of terrestrial sediment, the system ensures balance in elevation for possible sea level rise scenario. However, abrupt and/or rapid sediment input leading to partial burial of the trees may be detrimental to the trees development in the short term and the entire ecosystem in the long run. But how are ecophysiological processes affected before the mangroves trees die from partial sediment burial? What is the threshold below which normal tree functioning is ensured.The main objective of this study was to understand the impacts of disturbance on mangrove trees, as individuals and as an assemblage. Specifically the study targeted large sedimentation on selected ecophysiological processes (phenology, water transport), root development and general physiognomy and hence its impact on wood formation in mangroves. A survey was also done on the extent of wood exploitation and other human activities, in order to obtain background information on the environmental management in the area and hence to help create an integrated picture of the evolving mangrove ecosystem in the human-nature context.Main question: What is the significance of sedimentation in shaping the ecological status of mangrove forests? / Doctorat en Sciences / Author's maiden name: Judith Auma OKELLO / Due to a technical Di-Fusion bug it was not possible to input the correct date of the defense. The correct date is Thursday 30 June 2016. / info:eu-repo/semantics/nonPublished

Les tourbières ont stocké un tiers du carbone organique des sols mondiaux (C) malgré une superficie ne représentant que 3% de la surface terrestre. Cependant, en réponse aux changements globaux, les tourbières boréales et tempérées, majoritairement dominées par des sphaignes, peuvent être envahies par des plantes vasculaires susceptibles de modifier la dynamique du C dans ces écosystèmes. Cette thèse vise à étudier comment la présence des plantes vasculaires affecte le cycle du C des tourbières à sphaignes. Ces travaux ont porté principalement sur une plante envahissante de nombreuses tourbières, Molinia caerulea, via une étude en mésocosmes. Les expérimentations montrent que les plantes vasculaires sont à la fois favorables à la croissance des sphaignes et à la décomposition des litières. In fine, les résultats montrent que la présence de Molinia caerulea augmente la capacité de stockage du C dans les mésocosmes de sphaignes (30 to 220 gC stock m⁻² an⁻1), probablement liée à la forte productivité racinaire de cette plante. Cependant, cela semble s’opérer au détriment du C déjà stocké dans la tourbe avec une stimulation des microorganismes à travers la production d’exsudats racinaires. Ces derniers semblent également, d’une part promouvoir la consommation du C organique dissous et les émissions de CO₂ et de CH₄ observées en présence de Molinia caerulea, et d’autre part être responsables de la modification de la sensibilité à la température des exports de C via des changements des communautés microbiennes. L’impact de Molinia caerulea sur les microorganismes va aussi altérer ceux impliqués dans le cycle du N et entrainer une diminution des émissions de N₂O. / Peatlands have stored a third of the soil organic Carbon (C) in only 3% of the land area. However, in response to global change, boreal and temperate peatlands may shift from Sphagnum to vascular plant-dominated peatlands that may alter their C-sink function. This thesis aims at providing a better understanding of the vascular plants interactions in a Sphagnum dominated peatland and their implications on the C cycle. This work mainly focus on the invasion of a graminoid plant, Molinia caerulea, through a mesocosm experiment. Results from experiments show that vascular plants are both able to promote the growth of Sphagnum mosses as well as the decomposition of their litter. Molinia caerulea occurrence appears to increase the C sink capacity of Sphagnum peat mesocosms passing of 30 to 220 gC stock m⁻² y⁻1. This capacity of Molinia caerulea to store C is probably due to it high roots productivity. However, it also seems to stimulate the decomposition of ‘old’ C, stored as peat, by stimulating microorganisms activity through roots exudates. These latter also promote the dissolved organic C consumption and CO₂ and CH₄ emissions observed with Molinia caerulea occurrence, as well as the temperature sensitivity of C exports by altering the microbial communities. Molinia caerulea impacts on microorganisms also affect N cycle conducting to a decrease of N₂O emissions in these ecosystems.

L'hétérogénéité du paysage, définie par la composition en habitats et leur configuration spatiale, est considérée comme un facteur majeur affectant la biodiversité. Cependant, les effets de la composition et de la configuration sont souvent confondus du fait de corrélations entre les descripteurs de ces deux composantes. Il est crucial de déterminer leurs effets indépendants pour comprendre les processus qui contrôlent la biodiversité, et allouer les ressources dédiées à la conservation des espèces aux actions de gestion les plus pertinentes. L'objectif de cette thèse est, grâce à la mise en place de protocoles pseudo-expérimentaux dans l'ouest de la France, d'étudier les effets indépendant de la composition et de la configuration paysagère sur la richesse spécifique, la composition spécifique et la composition en traits fonctionnels des coléoptères carabiques et plantes vasculaires. Ces indices de diversité ont été mesurés au niveau du paysage (diversité gamma), et différentes représentations paysagères ont été testées pour comprendre le rôle de l'hétérogénéité de l'espace cultivé, au-delà de la seule prise en compte des habitats semi-naturels. Les résultats indiquent que l'hétérogénéité paysagère joue un rôle de filtre écologique sur les espèces de carabes et de plantes en fonction de leurs traits fonctionnels. La composition paysagère affecte la composition spécifique de ces groupes, les divers habitats hébergeant des communautés différentes. La configuration affecte la diversité des carabes en lien avec des processus possibles de complémentation entre habitats, tandis qu'elle n'a pas d'effet sur la diversité des plantes, qui ne semble donc pas déterminée par les processus de dispersion. Enfin, nos résultats soulignent que l'hétérogénéité liée aux habitats agricoles contribue à la diversité gamma.

L'hétérogénéité du paysage, définie par la composition en habitats et leur configuration spatiale, est considérée comme un facteur majeur affectant la biodiversité. Cependant, les effets de la composition et de la configuration sont souvent confondus du fait de corrélations entre les descripteurs de ces deux composantes. Il est crucial de déterminer leurs effets indépendants pour comprendre les processus qui contrôlent la biodiversité, et allouer les ressources dédiées à la conservation des espèces aux actions de gestion les plus pertinentes. L'objectif de cette thèse est, grâce à la mise en place de protocoles pseudo-expérimentaux dans l'ouest de la France, d'étudier les effets indépendant de la composition et de la configuration paysagère sur la richesse spécifique, la composition spécifique et la composition en traits fonctionnels des coléoptères carabiques et plantes vasculaires. Ces indices de diversité ont été mesurés au niveau du paysage (diversité gamma), et différentes représentations paysagères ont été testées pour comprendre le rôle de l'hétérogénéité de l'espace cultivé, au-delà de la seule prise en compte des habitats semi-naturels. Les résultats indiquent que l'hétérogénéité paysagère joue un rôle de filtre écologique sur les espèces de carabes et de plantes en fonction de leurs traits fonctionnels. La composition paysagère affecte la composition spécifique de ces groupes, les divers habitats hébergeant des communautés différentes. La configuration affecte la diversité des carabes en lien avec des processus possibles de complémentation entre habitats, tandis qu'elle n'a pas d'effet sur la diversité des plantes, qui ne semble donc pas déterminée par les processus de dispersion. Enfin, nos résultats soulignent que l'hétérogénéité liée aux habitats agricoles contribue à la diversité gamma. / Landscape heterogeneity, defined by habitats composition and their spatial configuration, is considered as one of the main factor affecting biodiversity. However, the effects of landscape composition and configuration are often confounded because of correlations between the descriptors of these two components. It is crucial to separate the effects of compositional and configurational heterogeneity to understand the ecological processes driving biodiversity and to allocate conservation resources to the most effective actions. Mensurative experiments were carried out in western France to assess the independent effects of landscape composition and configuration on species richness, species composition, and functional traits composition of carabid beetles and vascular plants. These diversity indices were measured at landscape level (gamma diversity), and different landscape representations were tested to address the role of the farmland heterogeneity, beyond the semi natural habitat / farmland matrix dominant representation. Results indicate that landscape heterogeneity act as an ecological filter on carabid and plant species according to their functional traits. Landscape composition affects species composition because different communities benefit from the various habitat types. In addition, landscape configuration influences carabid beetles diversity in relationships with possible complementation processes between habitats, but had no effect on plant diversity, suggesting dispersal was not a driving process of plant diversity. Furthermore, we found that the heterogeneity related to cultivated lands contributes to gamma diversity.