Nitric oxide (NO) is emerging as an important signalling molecule in plants. A major source of NO in planta is through the activity of nitrate reductase (NR),an enzyme required for nitrate reduction that can also reduce nitrite to NO. The model plant Arabidopsis thalianahas been extensively used to study mechanisms of NO production and signalling. Arabidopsis contains two isoforms of NR, NITRATE REDUCTASE 1 (NIAl) and NITRATE REDUCTASE 2 (NIA2). Increasing evidence suggests diverse roles for these proteins in NO production modulating plant development, biotic and abiotic stress tolerance. Low-oxygen or hypoxic stress, induced by periods of waterlogging or 'submergence, is a significant factor impacting plant and crop growth and survival globally. Terrestrial plants have evolved diverse mechanisms to cope with these stresses including alterations in gene expression, metabolism, morphology and physiology. In this thesis, Arabidopsis was used to as a model plant to investigate the putative regulation of these processes via NR and NO signalling. This investigation has focused primarily on analysing the initiation of stomatal closure, the formation of aerenchyma, and the induction of hypoxic gene expression in wild- type Arabidopsis plants and NIA gene knockout mutants. Waterlogging stress induced hypoxia in the root environment within 4 days, at which time stomatal aperture was significantly reduced in wild-type plants. In NIAI gene mutants, stomatal closure was completely abolished whilst closure occurred normally in the NIA2 mutant. Ethylene signal transduction and reactive oxygen species (ROS) production, mediated by ERECTA, ETRl, RBOHF, EIN2 and EIN3 were also shown to be critical for this response. The data suggest a role for NIAl in waterlogging stress induced guard cell NO generation. Under waterlogging stress conditions, stomata of wild-type plants were insensitive to exogenous NO, which functionally restored stomatal closure in NIAI and other mutants compromised in the stomatal response. A model is proposed whereby waterlogging stress induces ethylene and ROS signalling which acts upstream of NO production to regulate stomatal aperture during rhizospheric hypoxia. Aerenchyma is made up of gas spaces (lacunae) formed by apoptotic cell death of localised cells and is proposed to facilitate gas-exchange in submerged plant tissues. In Arabidopsis hypocotyls, prolonged waterlogging induced cell death leading to aerenchymous lacunae, as measured by anatomical analyses of hypocotyl sections. NR was not suggested to be required for cell death leading to aerenchyma, since NIA gene mutants exhibited equivalent lacunae formation to wild-type plants. A hydroponic cultivation system was employed to study hypoxic root gene expression. The upregulation of hypoxic tolerance genes, ALCOHOL DEHYDROGENASE 1 (ADHI) and HAEMOGLOBIN I(AHBI) was attenuated in a NIAI mutant and to a lesser extent in a NIA2 mutant over a 24 hour period of hypoxic stress, although whether this was attributed to NO production could not be confirmed. AffymetrixGeneChiptranscriptome profiling identified hypoxia-induced alterations in gene expression at 24 hours hypoxia in wild-type and NIA 1 mutant roots. Functional analysis of differentially expressed transcripts was performed utilising gene ontology annotations for the Arabidopsis genome. The analysis identified known hypoxia-associated processes significantly enriched amongst up or downregulated genes, and identified novel pathways directly or indirectly regulated by NIAl function. These cumulative data support an important role of NR and specifically NIAl in the regulation of hypoxic stress tolerance mechanisms at the physiological and molecular level.

Global average atmospheric CO2 concentrations are predicted to double before the end of this century. This increase has been predicted to raise global average temperatures, which in turn will increase atmospheric humidity. How plants will respond to these changes is an area of intense study. The variation within ecotypic responses of Arabidopsis thaliana to these environmental variables (C02, temperature and humidity) is explored in this thesis using a combination of morphological and novel environmental metabolomics techniques. This study utilises ecotypes of Arabidopsis thaliana originating from a range of altitudes and geographical locations to elucidate altitude-mediated variation In response to changes In environmental conditions. Morphological investigation shows that stomatal conductance is regulated by an interchangeable mechanism of stomatal density and stomatal aperture over a range of CO2 treatments and that elevated temperature or humidity can disrupt this mechanism. Furthermore, these characteristics of stomatal responses of Arabidopsis thaliana are shown to be independent of ecotypic altitude of origin. Environmental metabolomic analysis demonstrated clear separation between ecotypic rnetabolite fingerprints as well as showing correlations between ecotype altitude of origin and specific plant primary and secondary metabolites; providing novel elucidation of biochemical pathways involved in responses to environmental perturbation.

Important ecological processes happen over long periods of time and at the landscape scale. Effective conservation of biodiversity and management of natural resources and ecosystem services requires an understanding of these processes. Unfortunately, it is often impractical to conduct appropriate long-term, landscape-scale studies. Modelling offers an alternative approach. Complete ecosystems are too complex to model practically, but simulations of simplified systems provide useful insights of practical value. LandBaSE-P is an individual-based model for Puya hamata that provides information about impacts of fire on ecological processes in the páramo of the Reserva Ecológica El Ángel, Ecuador. Puya hamata is a flagship plant affected by fires and plays a key role in a number of ecological processes. This research found Puya hamata germinated much more frequently after fires, can form large aggregations of single recruitment cohorts, suffers very low mortality (with and without fires) once established, and lives up to 28 years. The spatial aggregation of Puya hamata plants reduced effective reproductive output, consistent with the theory that pollinator behaviour around large groups of Puya plants reduces cross-pollination, leading to inbreeding depression and poorer seed viability and germination. Puya hamata’s population structure can be an indicator of recent fire regime. LandBaSE-P simulations showed that population size is not affected by rare, long-distance seed dispersal. However, in the simulations of páramo grasslands, Puya relative germination is maintained in high numbers by burning. Puya hamata has an important role in ecology and biodiversity. The model LandBaSE-P is a complementary tool for conservation and sustainable land management. This thesis shows how fieldwork combined with laboratory studies and modelling, can provide a good understanding of complex dynamics of real-world populations, and generate ideas for management and future research.

Plants are continuously exposed to different abiotic and biotic stresses in their natural environment. Their capacity to survive depends on the capacity to perceive external signal and quality amount a defence response for protection from the stress perceived. The purpose of this project was to study the impact of combined abiotic stress and biotic stress on the outcome of the disease inducing Arabidopsis thaliana – Pseudomonas syringae interaction. This study included a focus on the role of ABA in these interactions and also whether 3´-O-β D- ribofuranosyl adenosine (hereafter it called ‘400’ compound), a novel adenosine derived compound induced during compatible interactions, was involved. The later involved the targetted disruption of a putative 400 biosynthetic pathway involving analysis of knockout mutants of enzymes; APD-ribose diphosphatase NAD binding / hydrolases of the NUDIX class, glucosyl transferases, ribosyltransferases, a ribose-phosphate pyrophosphokinase3 and galactosyltransferases. Unfortunately, none of these targeted interventions modified the host response to Pseudomonas infection, nor altered levels of 400 in challenged leaves. The primary research investigated the interaction between abiotic and biotic stresses in Arabidopsis plants focussing on the modulation of plant defence against multiple, and possibly antagonistic, stress responses and the role plant hormones play in this process. We showed that high light caused enhanced susceptibility to the already virulent Pseudomonas syringae DC3000pvsp61. The pathways contributing to this enhanced susceptibility were largely ABA independent. Subsequent characterization of transgenic lines expressing the soluble Arabidopsis abscisic acid receptors, PYRABACTIN RESISTANCE1-LIKE4-6 provided compelling evidence for a role for these receptors in DC3000 virulence strategies, but they contribute to a lesser extent to the enhanced susceptibility under high light. This was corroborated genetically by using mutants of the immediately downstream targets of PYLs, the type two protein phosphatase, specifically the triple mutant hab1-1/abi2-1/abi1-2. A number of epitope and fluorescent constructs were generated to facilitate future studies of the role of ABA signaling. Targetted profiling suggested that SA dynamics were altered under DC3000 challenged Arabidopsis grown under high light. Furthermore, differential accumulation of flavonoids suggested these may also play a role in attenuating host defences under high light. Finally we provide evidence based on comparative analysis of that the photoreceptors phytochrome double mutant phyA-211/phyB-9 and cry1/cry2 behave antagonistically in Arabidopsis response to DC3000. Overall our studies support the conclusion that plants abiotic stress (HL) response takes precedence over biotic stress (DC3000) responses and that abiotic stress is detrimental to plant immunity. The luciferase transgenic PYL lines showed high level of expression of ClucP::PYL5 plant tissues challenged 2hpi of DC3000 (OD600: 0.15) in comparison with C1lucP::PYL6. This result opposes to what RT-PCR reported; which was that three PYLs genes display similar expression level at 6hpi of hrpA or 18hpi of DC3000. The epitope tags of CaMV::HA transgenic plants showed HA-tagged signal with stunted phenotype in a range of PYL4, 5 and 6 plants but none of the plants displayed any differences in susceptibility to DC3000. Although, RT-PCR assay showed high levels of expression in the three PYLs, 6hpi of hrpA but no signal was detected in B8eGFP::PYL5 transgenic line either followed the DC3000 and hrpA infection or by examined plant seedlings at early stages under confocal microscopy.

Le Miscanthus x giganteus est une culture pérenne, nouvellement produite en Europe et présentant un intérêt fort pour son usage énergétique. Son implantation présage donc une réorganisation territoriale pérenne. Pour anticiper cette réorganisation, de nombreuses études modélisent les dynamiques spatialement explicites de son insertion. Notre thèse se positionne dans ce courant de recherche. Celle-ci vise à proposer un nouveau cadre de modélisation des processus de décision des agriculteurs, permettant la dissémination horizontale (scaling out) de ces processus issus d’études de cas, vers des territoires élargis. Pour cela, la thèse exploite le modèle du raisonnement à partir de cas. Elle articule (i) une démarche d’acquisition de connaissances sur les processus de décision des agriculteurs relatifs à l’insertion territoriale du miscanthus et (ii) la conception et évaluation d’un prototype ad hoc de raisonnement à partir de cas. La phase d’acquisition des connaissances montre que le processus d’insertion territoriale du miscanthus est complexe : celui-ci est étroitement lié aux contraintes parcellaires du territoire. Ces connaissances nous conduisent alors à discuter du choix des variables biophysiques et humaines intégrées à ce jour dans les modèles spatialement explicites. La phase de conception et d’évaluation du prototype de raisonnement à partir de cas montre que le modèle du raisonnement à partir de cas est particulièrement bien adapté pour modéliser un phénomène contextualisé. Evalués sur nos données d’enquêtes, ces résultats nous conduisent à discuter des modalités d’application du prototype sur d’autres bassins de production de miscanthus / Miscanthus x giganteus is the perennial crop, newly produced in Europe. Even if miscanthus is not so heavily produced nowadays, this crop would be of great interest for energy use. However, the allocation of miscanthus could produce a sustainable reorganization of the landscape. Therefore, many studies aim to model the land use change caused by miscanthus, in order to identify sustainable supply areas: our research belongs to this field. In our research, we propose a new framework for modeling decision-making process of farmers, relying on scaling out. More accurately, we propose to use the case-based reasoning model which solves problems based on an analogical reasoning. Then our research is structured: (i) by a knowledge acquisition step about decision-making process of farmers, based on farm surveys, conducted in the Côte d'Or department (Burgundy region) and (ii) by the design and evaluation of an ad hoc prototype of case-based reasoning. On the one hand, results of knowledge acquisition phase show that miscanthus allocation process is complex, more accurately, that miscanthus allocation process is closely related to land constraints, particularly in terms of logistic and environmental preservation of plots. These results lead us to discuss the selection of biophysical and human variables included to the current spatially explicit models. On the other hand, the design and evaluation phase of our prototype shows that case-based reasoning is particularly well suited to model a contextual phenomenon. These results lead us to discuss the modalities for implementing the prototype in other production areas of miscanthus