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La fertilisation microdose (FM) est promue en Afrique subsaharienne pour booster la productivité agricole. Cette technique consiste en l’apport localisé de petites quantités d’engrais (2 à 6 g / poquet) aux pieds des plants après la levée. Cependant, la variabilité de la réponse des cultures à la FM peut constituer une barrière à son adoption. Par conséquent, une méta-analyse et des essais agronomiques sur 539 parcelles de producteurs ont été réalisés afin d’identifier les facteurs déterminants la variabilité de la réponse des cultures à la FM au Burkina Faso. Il a été mis en évidence que la réponse de la FM augmente avec la disponibilité en eau, que ce soit à travers la pluviométrie ou la mise en place de techniques de conservation de l’eau du sol. De manière spécifique, les meilleures réponses ont été observées sur les sols de meilleure fertilité inhérente que sont, suivant la classification endogène des sols, les sols noirs, les sols argileux et les sols situés dans les lits majeurs respectivement en zone de pluviométrie de 800 - 1000, de 600 - 800 et de 500 - 600 mm. De manière plus générale, les meilleures réponses ont été observées sur les parcelles qui ont bénéficié de précédents apports modérés d’engrais. Les faibles réponses ont été observées d’une part, sur des parcelles de profondeur de sol < 40 cm, présentant des problèmes d’engorgement d’eau ou un trop faible niveau de fertilité et d’autre part, sur les parcelles ayant bénéficié d’importants apports précédents d’engrais et/ou sur les parcelles nouvellement défrichées. Comparé à la FM appliquée seule, il a été observé une tendance à la réduction de l’effet de la FM lorsqu’elle est combinée avec des amendements organiques (compost, biochar). Ces résultats ont permis d’établir des recommandations pratiques à l’intention des producteurs. D’autres investigations sont cependant nécessaires pour affiner la compréhension de la variabilité de la réponse à la FM., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Cancer progression is influenced by the physico-chemical features of the tumor microenvironment. Considered as a major hallmark of cancer, tumor acidosis results from an exacerbated glycolytic metabolism and an insufficient clearance of protons by the vasculature. Hence, tumors have been described as more acidic than healthy tissues. Cancer cells will shift their metabolic preferences from glucose towards fatty acids (FAs) to adapt to this hostile environment and thereby will gain further advantages to survive, proliferate and metastasize. We examined whether promoting an excess uptake of specific FAs could lead to antitumor effects in these acidosis-adapted cancer cells. We found that n-3 but also n-6 polyunsaturated FAs (PUFAs) selectively induced ferroptosis in cancer cells under ambient acidosis. Upon exceeding the buffering capacity of lipid droplets, n-3 and n-6 PUFA peroxidation accounted for cytotoxic effects and even more so if their storage or beta-oxidation was inhibited. Finally, an n-3 PUFA-rich diet significantly delayed mouse tumor growth when compared to a control diet. The therapeutic potential of PUFA supplementation was further evaluated by studying the administration of n-3 PUFA-rich capsules to human volunteers. Altogether, our data point out dietary PUFAs as a selective adjuvant antitumor modality that may efficiently complement pharmacological approaches., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Les études récentes sur la fertilisation microdose ont noté une variabilité de la rentabilité économique dont certaines sources sont inconnues. L'objet de cette thèse est d'identifier les facteurs socio-économiques explicatifs de la rentabilité économique de la fertilisation microdose assortis de stratégies d’adaptation et de mitigation des risques. Avec des approches économétriques et des données primaires et secondaires, les résultats montrent que la fertilisation microdose peut contribuer à une augmentation significative du rendement du maïs et du sorgho. Ceci requiert que les producteurs aient une main-d’œuvre disponible et un accès aux engrais minéraux et à la formation. Ces facteurs affectent les décisions d’adoption des producteurs et permettent d’expliquer les différences de rentabilité économique observées entre les adoptants. En dehors du warrantage et de la mécanisation, des stratégies endogènes sont aussi envisageables par les producteurs pour minimiser les effets des facteurs de risque liés à la fertilisation microdose. Ceci implique que les décideurs politiques devraient promouvoir le warrantage, accélérer la mécanisation et appuyer le renforcement de capacités des organisations rurales., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Rice stripe necrosis virus (RSNV) is the causal agent of the rice crinckle disease. Considered as an (re-)emerging virus in South America and West Africa, little data are available on the virus, and especially how the virus interact with its host plant and its plasmodiophorid vector, Polymyxa graminis. The tripartite interactions between RSNV, P. graminis and Oryza sativa has been investigated to confirm experimentally the acquisition and transmission of the virus by this vector protist. The analysis of the genetic diversity of the new sequences obtained, presents two main lineages of RSNV emerging in America and re-emerging in Africa. The genetic diversity of the RNA2 segment of RSNV and BNYVV were similar except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene, whereas the RNA1 segment showed higher nucleotide variability for RSNV than for BNYVV. The RSNV transmission vector, P. graminis f. sp. colombiana, was found highly associated with Oryza sativa and O. glaberrima, but is also found, to a lesser extent, on a wider host range including Zea mays, Sorghum bicolor, Pennisetum glaucum, and Triticum durum as well as with some rice field weeds. while Polymyxa multiplies in different hosts, the virus is only transmitted to rice. Sequences of the 28 S, beta tubulin, eF1- alpha, L10 and RSP5 40s genes have been used in addition to the full-length sequences of ITS, and 5.8 S to propose a multi-locus sequence analysis as a tool for the precise diagnostic of rice associated Polymyxa. In this thesis, a first demonstration of the acquisition and transmission of RSNV by P. graminis under experimental conditions. The thesis is now opening the field for screening rice varieties for resistance against the virus and/or its vector, as well for proposing biologically based management strategies for the rice crinckle disease., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

For plants and especially for maize (Zea mays), experiencing water deficit at key phenological stages can cause critical yield losses. As such, there is a need to understand the complex plant hydraulic behavior in constraining environments. Within plant diversity, landraces may hold root systems hydraulic architecture that are well fitted to specific pedo-climatic environments. Their sets of traits could be "key" candidates to promote sustainable farming practices and alleviate the consequences of drought episodes. However, due to the difficulties of quantifying the root hydraulic anatomy, there is a knowledge gap in the identification of suitable combinations of root traits. Therefore, developing new ways to explore and evaluate the influence of root hydraulic anatomy on water uptake will be beneficial. In this thesis, we advance our understanding on hydraulic anatomy influence at different scales and for specific soil and environmental constraints. Firstly, we created a new way to estimate root hydraulic properties. Secondly, we developed a method to generate root hydraulic atlases based on a combination of root cross-section images and modeling tools. Then, we investigated in silico the crucial role of root anatomy, subcellular hydraulic properties and maturation stages on water uptake. It showed that the root radii, the contribution of aquaporins to the cell membrane permeability and root maturation rates can create contrasted uptake patterns and influence the cumulative water uptake of in silico maize plants. These exploratory findings inform potential candidate sets of traits which could be investigated furthermore., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Intercropping consists in growing distinct crops on the same plot at the same time. It may play a role in the transition to sustainable agriculture thanks to its benefits, e.g. higher yield, lesser use of pesticides. Intercropping has experienced a particular boom in recent years in market gardening and there are now countless mainstream market gardening books dealing with it. However, its use by professional market gardeners remains low. The most likely reason is that intercropping is more complex than the image conveyed by these books and very little objective data is available to help market gardeners in its relevant implementation. This thesis tackles the issue of intercropping in market gardening with the aim of providing market gardeners with knowledge and reliable information enlightening management choices. We begin by listing the interactions observed in intercropping, both between the associated crops and with their environment, and present them as networks. We then investigate the prediction of intercropping outcome based on complementarity principles by comparing the results of various intercrops in on-field trials. We show the importance of the difference in sowing date, growth dynamics and maximum soil coverage between crops in the determination of yield gain and yield gain asymmetry in intercrops. Finally, we address the issue of yield inter-site variability by comparing the growth of three intercrops in different farms, using participatory trials. We explain our methodology and show the consistency of intercrops relative yield in a range of environmental conditions and crop management practices. Our approach is purposely exploratory. This thesis paves the way for the scientific study of intercropping in market gardening and highlights some key points for the use of intercropping by market gardeners., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Arctic warming and permafrost loss modify northern ecosystems through soil subsidence, changes in soil hydrology, nutrient availability and vegetation succession. In particular, warming and soil moisture conditions influence Arctic tundra vegetation production and distribution: wetter soil conditions favor sedge expansion and drier soil conditions drive woody shrub expansion. While these shifts in vegetation may alter permafrost integrity by modifying the surface energy transfers, they may also be responsible for further changes in the tundra vegetation production and distribution by influencing plant nutrient cycling. Specifically, this PhD thesis investigates the influence of permafrost degradation on mineral nutrient distribution in soils and the influence of tundra vegetation shift on mineral nutrient cycling. Along a permafrost thaw gradient in Interior Alaska, our results demonstrate that permafrost is an important frozen reservoir of nutrients for plants, with stocks of total and exchangeable base cations in the permafrost soil layers more than twice as high as in the seasonally thawed active layer. Moreover, we observe that foliar elemental stocks and annual fluxes from leaf to soil litter change with vegetation shift; sedge expansion promotes Si, P and Fe foliar cycling and shrubification promotes Ca and Mn foliar cycling. Lastly, we highlight that shrub and sedge species both take up nutrients from deeper soil horizons upon permafrost thaw, with the deeply rooted sedge benefitting first from the release of nutrients at depth. These findings provide insights to improve the integration of changes in mineral nutrient cycling into models predicting Arctic ecosystem evolution and feedbacks on climate., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

The phage replication cycle begins with its adsorption to its host and ends with the release of new virions upon bacterial lysis. These steps are important, not only for the proper conduct of the phage life cycle, but also because proteins mediating attachment and lysis have a significant biotechnological potential. The adsorption step involves viral proteins called receptor binding proteins (RBP) and specific receptors at the host surface, while membrane permeabilization and cell wall degradation leading to lysis are achieved by the concerted actions of holins and endolysins. This thesis aimed to better understand the adsorption and lysis processes of phages targeting the Bacillus cereus group. The first part of this work showed that phage Deep-Blue is a promising candidate for controlling emetic strains, although its narrow host range requires its integration in a phage cocktail. In the second part, the viral proteins involved in the adsorption process were investigated. Comparison of the tail proteins of B. cereus siphoviruses revealed diverse genetic organizations and the prevalence of carbohydrate binding modules (CBM). The role in adsorption of these CBM was experimentally demonstrated for phage Deep-Purple. Regarding myoviruses, Deep-Blue and Vp4 RBP were identified, and their tail regions compared to that of the well-known Listeria phage A511 revealing important differences in key proteins. The third part of this thesis showed that different lysis mechanisms are present in phages infecting B. cereus and that endolysins have a broader activity spectrum than their related phages revealing that they could be used in biocontrol and detection., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Forests contain more carbon (C) in biomass and soils than is stored in the atmosphere. Consequently, forests are at the forefront for C sequestration and storage in the framework of climate mitigation. The European Union has recognized C storage in forests as one of the key policy options to achieve climate neutrality by 2050. To accomplish this objective necessitates implementation of efficient and effective forest management measures to enhance the C storage capacity of forests. However, previous studies on the impact of management measures on forest C storage mostly occurred in single forest and/or focused on one ecosystem component. Therefore, there is paucity of robust and generalizable information about the impact of key forest management measures on C storage and distribution in multiple forest ecosystem components to guide forestry in Europe. This thesis investigated the impact of tree species identity and mixing on C storage and distribution in aboveground woody biomass, coarse roots, and soil ecosystem components in 21 forest triplets (two-species mixed forest and their respective monocultures at the same site) in seven European countries. The triplets consisted of Scots pine (Pinus sylvestris), European beech (Fagus sylvatica L), and Oak (Quercus robur L/ Quercus petraea (Matt.) Liebl.). The broadleaved forests (European beech, oak) increased C storage in above and belowground woody biomass more than Scots pine, but the opposite was observed for soil C storage. Considering total C stocks (aboveground + coarse roots + soil), the mixed forests were at least equivalent to the most performing monocultures, implying that mixed species forestry may not compromise total C storage., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Lignin is the most abundant source of renewable aromatics on Earth, but its tendency to undergo irreversible condensation reactions during lignocellulose pretreatment hampers its valorization in current biorefinery schemes. A strategy for circumventing this issue is the so-called reductive catalytic fractionation (RCF), which relies on the use of redox catalysts and hydrogen gas to promote the reductive cleavage of lignin and to prevent lignin condensation, ultimately yielding low-molecular weight phenolics, along with a delignified (hemi)cellulose fraction. Some limitations must be overcome to improve the potential of RCF. The treatment of biomass feedstocks alternative to the widely explored virgin wood is important for extending the range of applications of this method. In addition, the recurrent adoption of high pressures of hydrogen gas poses safety and equipment constraints. This dissertation reports on research undertaken to investigate the RCF of wheat straw, an inexpensive and abundantly available agricultural residue, with a focus on the study of hydrogen-free process configurations. Moreover, an innovative dithionite-assisted organosolv fractionation (DAOF) method for the reductive depolymerization of lignin within biomass pretreatment is developed, based on the use of sodium dithionite as a reducing agent, instead of hydrogen gas and redox catalysts. Overall, this dissertation shows that RCF and DAOF represent promising approaches for the sustainable production of light aromatics via the reductive depolymerization of lignin., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Dry hopping has become a trend in the production of hoppy beers. During dry hopping, aroma compounds are less susceptible to be lost or transformed compared to a kettle hopping. However, many non-volatile substances are potentially harmful for the beer quality. The impact of these non-volatile substances on the beer taste and its stability through aging was investigated in this thesis. In the fresh product, we showed at which point cis-humulinones (up to 13.3mg/L) contributed to beer bitterness. We also confirmed the importance of terpenols (up to 499µg/L of linalool and 53µg/L of geraniol), polyfunctional thiols (up to 0.3µg/L of 3SHol, 2.1µg/L of 3SHA and 3.2µg/L of 3S4MPol) and several esters for dry-hopped beer aroma. After two years of aging, cis-humulinones were rapidly degraded (average residual levels of 27%). Considering the structure of cis-humulinones degradation products, it should not be a simple problem of oxidation. The degradation processes of linalool and geraniol (average residual levels of 57 and 45%) were also questioned. On the other hand, it is indeed oxidation that explains the degradation of polyfunctional thiols (average residual levels of 29% for 3SHol and 17% for 3S4MPol), the color increase (correlated to the initial levels of catechin and epicatechin, R²=0.96) and the colloidal instability (correlated to the initial levels of flavan-3-ol dimers and trimers, R²=0.79) of dry-hopped beers. The hop enzymatic activity was equally suggested as a potential source of instability. Besides the hop diastatic activity over beer dextrins, an esterase activity capable of degrading fermentation esters was demonstrated. Considering the deleterious effect of several non-volatile hop compounds, research of new ways to produce hop extracts dedicated to dry hopping and exempt of undesired compounds is advised to improve and maintain the quality and stability of dry hopped beers., Le houblonnage à cru est devenu tendance dans la production de bières aux arômes houblonnés. Lors de l’ajout à froid, les arômes courent moins de risque d'être perdus ou transformés que lors d’un houblonnage traditionnel. Toutefois, plusieurs composés non volatils co-extraits sont potentiellement dommageables pour la qualité de la bière. L’impact de cette fraction sur sa flaveur et sa stabilité lors du vieillissement a été investigué dans le cadre de ce travail. Pour les produits frais, nous avons montré combien les cis-humulinones (jusque 13,3mg/L) participaient à leur amertume. Nous avons aussi confirmé l’importance des terpénols (jusque 499 et 53µg/L de linalool et de géraniol), des thiols polyfonctionnels (jusque 0,3, 2,1 et 3,2µg/L de 3SHol, de 3SHA et de 3S4MPol) et de différents esters pour leur arôme. Après deux ans de vieillissement, les cis-humulinones se dégradent très rapidement (teneurs résiduelles en moyenne de 27%). Au vu de la structure des produits de dégradation identifiés, il ne s'agit pas simplement d'un problème d'oxydation. Le mode de dégradation du linalool et du géraniol (teneurs résiduelles en moyenne de 57 et 45%) ont été aussi questionnés. C'est par contre bien l'oxydation qui explique la dégradation des thiols polyfonctionnels (teneurs résiduelles en moyenne de 29% pour le 3SHol et de 17% pour le 3S4MPol), la prise de couleur (corrélée aux teneurs en catéchine et épicatéchine, R²=0,96) et l'instabilité colloïdale (corrélée aux teneurs en dimères et trimères de flavan-3-ols, R²=0,79) des bières houblonnées à cru. L’activité enzymatique du houblon s’est avérée aussi être une source potentielle d'instabilité. Outre l'activité diastasique sur les dextrines de la bière, une activité estérase a été mise en évidence. Etant donné l’effet délétère de nombreux composés non-volatils du houblon, il semble opportun de rechercher des voies de production d’extraits dédicacés au houblonnage à cru et dépourvus de composés indésirables., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Climate change and its consequences stand before us as the greatest challenge of our generation. The Arctic is warming at unprecedented rate and permafrost thaw is leading to irreversible changes with a global influence on climate. Permafrost carbon reservoir is twice as large as what is stored in the atmosphere. Upon thawing, permafrost organic carbon is vulnerable to be degraded by microorganisms resulting in additional greenhouse gas emissions. How fast and how much carbon will be released to the atmosphere with permafrost thaw remains highly uncertain. Mineral surfaces and cations can stabilize organic carbon in soils and sediments and mitigate its degradation as greenhouse gases. Yet, the interactions between minerals and organic carbon in permafrost and the consequences of changing soil conditions upon thawing are still poorly understood. This Ph.D. thesis tackles the influence of permafrost thaw on mineral organic carbon interactions and investigates how changing soil conditions may promote or mitigate organic carbon stabilization mechanisms. We found that up to 59% of total organic carbon is potentially mineral-protected. We observed that abrupt thaw increases the supply of stabilizing surfaces and cations. Upon gradual thaw, we highlighted that redox interface greatly influences the location of hotspots for mineral organic carbon interactions. These findings highlight that mineral organic carbon interactions can protect organic carbon despite permafrost thaw. We argue that mineral organic carbon interactions should be investigated together with other factors and included in the next generation of Earth System models to better predict climate trajectories., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

The Great Barrier Reefs (GBR) is a treasure of biodiversity, with an immense ecological, economical and iconic value. However, this unique ecosystem is facing many threats, and is particularly suffering from global change. Management measures are therefore more than ever required to protect and restore the reefs. By reproducing both the ocean circulation and dispersal processes, biophysical models can help to inform and support such management measures. However, model outputs always come with a certain level of uncertainty, potentially impeding their reliability. Among others, the spatial resolution of ocean circulation models can affect the overall quality of their outputs. In this thesis, we use the 2D version of the multiscale coastal ocean model SLIM to assess the effect of spatial resolution on the whole modelling sequence. We hence compare the outputs of various model setups with five resolutions ranging from 250 m to 4 km. While the tidal signal is similar for all resolutions, strong discrepancies appear for simulated current velocities, especially over reefs and in their close vicinity. This in turn affects the dispersal pattern of virtual particles, leading to significant cumulative differences over multiple weeks. In a second stage, we also show that coral connectivity indicators inferred from larvae dispersal simulations vary with the resolution of the model. We hence underline the importance of using a resolution fine enough to represent the processes of interest when using models to support reef management. As a last step, we evaluate the footprint of sediments that would be released from a coal mine project adjacent to the GBR. We demonstrate that fine sediments could have far-reaching impacts on seagrass meadows, a dugong sanctuary, and important turtle nesting beaches. Throughout the thesis, we underline how processes happening at a small-scale influence in turn those happening at larger scales in coral reef environments., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Plant root systems are responsible for the capture of soil water and minerals essential for their growth. With the need to reduce fertiliser use and improve resilience to extreme climate events, improving resource capture efficiency has become a hot topic in agriculture. This includes optimising root distribution in soils via appropriate root system architecture and growth. Root systems are often described using integrative variables, e.g. number and biomass, that are cost-effective but provide limited cues on root distribution. Modelling studies have shown that root systems can also be described using process variables, depicting growth and development processes. These are expected to be more closely connected to the underlying biology than the integrative variables and to lead more directly to optimisation paths. In this thesis, we created a novel high-throughput phenotyping pipeline of plants grown in aeroponics. This pipeline exploits high spatial and temporal resolution image series to estimate process variables from simple morphologic features, with very limited computing resources. It was used to analyse the genetic architecture of process and integrative variables on diversity panels of bread and durum wheat (500 genotypes) and was evaluated against independent experiments (pouches, rhizotubes and field). We demonstrated that process information can be estimated easily from simple morphologic features if dense time series are available. We also showed that lateral root formation, despite being highly variable along the root system, can be constant when cumulated at the whole plant level. Cross-experiment validation revealed that genotypic differences for process variables were largely environment-specific. Finally, the genetic architecture of process variables was not found to be simpler than that of the integrative ones., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Plant transpiration is the main component of terrestrial evapotranspiration and represents about 60% of terrestrial rainfall. This huge amount of water is extracted from the soil by the plant root systems, which thereby play a crucial role in controlling soil moisture (SM) and its variability in time and space. Functional-structural root-soil models (FSRSMs), which combine root functional and structural information have been developed to simulate carbon, water and nutrient transfers between plants, atmosphere and soils. These models can therefore help predict the impact of plant root architecture and the distribution of soil and root hydraulic properties on root water uptake (RWU) and investigate the key factors determining SM and RWU variability. This PhD thesis is a combination of three-dimensional simulation at the plant scale and experimental work at the field scale to advance our comprehension of the hydraulic resistances in the soil-plant system that control transpiration and RWU. First, the 3D FSRSM R-SWMS was validated by combining root and tracer distributions obtained by magnetic resonance imaging (MRI) to inverse modeling. Second, we demonstrated the importance of rhizosphere resistance on the relationship between plant transpiration and leaf water potential. This result was obtained by using an FSRSM to represent the experimental behavior of two Maize genotypes (with and without root hairs). Finally, a field scale experiment highlighted that plant associations with complementary root systems did better tolerate water deficit than other associations by exploiting specific depth niches., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Xylella fastidiosa, a plant-pathogenic bacterium colonizing xylem and transmitted by insects, is involved in severe outbreaks worldwide. X. fastidiosa establishes in a wide range of conditions including different host plants and vector species, making it highly unpredictable in not yet colonized areas. A quarantine agent in Europe, it has recently been reported as a pest in several Mediterranean European areas, raising questions about the risk of a potential expansion up North. This work investigates the possibility of X. fastidiosa establishing in northern temperate Europe by examining the potential host range and potential insect vectors in these areas. Three different tools were used to investigate host range: mechanical inoculation, transmission via infected vectors, and sentinel plantation. These trials revealed that the Salicaceae include suitable host species that can be colonized by the bacterium, such as Populus tremula and Salix alba. On the other hand, the mobility of two potential insect species for these regions was investigated: Philaenus spumarius and Aphrophora salicina, through flight-mill and mark-release-recapture experiments. Driven by willow distribution, A. salicina proved to be a good flyer. Associated with Salicaceae, this species could transport the bacterium over medium or long distances on plants forming linear corridors in riparian areas or in alignments along crops. These environments could act as reservoirs from which polyphagous vectors as P. spumarius could transmit the bacterium on a local scale to economically important crops. This study highlights one possible scenario and pathosystem for potential long-term establishment and spread of Xylella-related diseases in northern temperate Europe., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

The Kapuas River delta (KRD) is a low-lying marshy delta on the western coast of Borneo Island, Indonesia. In the last decades, palm oil cultivation and forest fires have encroached on the Kapuas water catchment areas, changing the Kapuas hydrological regime and triggering more intense flooding in the KRD. Meanwhile, climate change has also rendered flooding events in the delta less natural and more disastrous. As population density rises, flooding risks attributed to riverine and coastal surges must be properly assessed. The importance of this assessment for urban planning and coastal protection development cannot be overstated. However, as in most developing countries, local water managers in the KRD lack data and tools to assess flooding risks properly. Consequently, the mechanisms that drive the flooding events in the KRD remain poorly known. Creating robust forecasting to predict flooding events is challenging with the lack of observational data, even more so with limited computational resources. The first objective of this thesis is to investigate the impact of the interaction between tides, storm surges, and river discharges in the KRD, particularly in the densely-populated city of Pontianak, which lies on the delta. The interactions between the driving forces and the effects on compound flooding are simulated using a hydrodynamic model (SLIM). Then, based on the maximum water-level profile, compound flooding hazard zones along the Kapuas River are delineated. In the second phase, this thesis combines the process-based and data-based modeling approaches to tackle the issue caused by limited computational resources and observational data. The process starts with building a hydrodynamic model to run flood scenarios in the KRD. The next step is to create machine learning (ML) models and train them using the outputs of the hydrodynamic model to predict water levels and future floods. Several ML algorithms are evaluated to ensure that the ML model is robust. Rando, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Cultivated yam (Dioscorea rotundata) is a staple tuber crop in West Africa that is mainly propagated vegetatively. Although the majority of yam cultivars flower, the control of its sexual reproduction - in particular sexual expression - remains largely unknown despite its importance for breeding programs. Our objectives were to: 1) characterize the flowering phenology and identify the causes of sex variation in this species; 2) analyze the genetic and hormonal controls of sex determinism; and 3) study the performance of sexual reproduction in monoecious cultivars. Our histological study showed that during floral morphogenesis, stamen and carpel primordia are initiated in all flowers irrespective of sex, but while only primordia corresponding to the sex of the flower continue to develop in sex-stable plants, male and female flowers of sub-dioic populations retain remnants of organs of the opposite sex. Our results also showed that the sex variation of the offspring was more related to the sex of the parents (monoecious in this case) than to the tuber sections used as seed tubers. Our genetic study did not identify a clear genetic marker for early determination of sex identity in D. rotundata yams from Benin but supported the involvement of a genetic locus (Z-) in sex expression with a possible transition from a ZZ/ZW female heterogamous system to an XX/XY male heterogamous system. Our hormonal analyses showed that jasmonates (MeJa) had a masculinizing effect in monoecious plants and that application of MeJA and cytokinins (BAP) accelerated flowering and increased inflorescence production. Furthermore, our crossing results showed that flowers of monoecious plants were fertile and showed a reproductive performance comparable to that of dioecious plants, so that they can partially compensate for the scarcity of female flowers in breeding programs. Altogether, our study has improved our understanding of the control of sex in cultivated yam (Dioscorea rotundata)., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Oxidative cleavage involves the rupture of carbon-carbon double bonds in alkenes for the production of carbonyl compounds of high added value. Most of the works related to this matter are focused on small and aromatic alkenes, but only few of them address unsaturated fatty acids (UFAs). Yet UFAs can be cleaved into dicarboxylic acids, eventually with an odd number of carbon atoms rare in nature and highly demanded for polymer and pharmaceutic applications. This is typically the case of azelaic acid accessible by oxidative cleavage of oleic and linoleic acids, making these reactions particularly interesting. To date, the oxidative cleavage of UFAs is mainly performed by ozonolysis which is high energy demanding process with several risks associated to ozone handling. The other alternative is related to the use of transition metal catalysts in homogenous phase which are quite active in terms of conversion and yield, but they are pollutant and cannot be recovered. On the other hand, current heterogeneous catalysts display poor activity due to the poor contact amid the UFA and the active phase. To solve this issue, we propose new heterogeneous catalysts formed by oxidized carbon black (CBO) and calcined carbon submicrometric particles (CCN) functionalized with polydopamine (PDA). The latter is a polymer with amine and catechol groups which act as tweezers for the complexation of metal cations. These functionalized carbon supports were impregnated with Ru which is a transition metal quite active in the oxidative cleavage reaction. All catalytic tests were carried out with oleic acid in a biphasic solution formed by H2O/MeCN/AcOEt (4/2/1) at room temperature with NaIO4 as oxidizing agent. These catalysts completed the transformation of oleic acid into pelargonic and azelaic acids after 7 h of agitation. Moreover, they remained active even after 5 consecutive catalytic tests demonstrating their stability. Further characterization showed that the solid catalysts released Ru, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Heterogeneous catalytic epoxidation of olefins is of considerable fundamental and industrial interest. A particular family of metal oxide clusters called polyoxometalates (POMs) have shown considerable success in green catalytic oxidation reactions. Heterogenization of POMs with organic ligands has proved to be an attractive strategy to form epoxidation-active hybrid catalytic materials. This thesis presents fundamental and applied approaches to the hybridization of a Keggin POM with bipyridine, a hydrophobic ligand with robust redox properties, yet largely unexplored, for the selective epoxidation of olefins with H2O2. A systematic investigation of hybrid catalysts composed of Keggin PW12O403- and substituted bipyridines, highlights the role of the hybrid constituents in the epoxidation reaction. A pre-activation strategy, at the synthesis level, consisting in contacting the Keggin anion with H2O2 prior reaction with the ligands, is conducted to boost the catalytic epoxidation. The catalytic behaviour of the pre-activated hybrids is inspected in details and their structures are solved by single crystal X-ray diffraction. A reaction mechanism is proposed that highlights the pivotal, yet often underestimated, role of H2O2 in the reached catalytic performances. The active species responsible for the oxygen transfer to the olefin is a hydroperoxide intermediate species which is formed by interaction between the anionic structure of the catalyst and H2O2. The latter operates as a “conservative agent” whose presence in the catalytic system is required to prevent the catalysts from deactivating irreversibly., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Approximately 800 million people populate areas within 100 km of a potentially active volcano. Since the beginning of human settlements, communities in volcanically active regions have enjoyed various benefits from volcanic eruptions, notably the occurrence of volcanic soils with outstanding agricultural capabilities. However, these populations are also exposed to the potentially disastrous impacts of volcanic hazards, of which tephra fall produced during explosive activity is the most frequent and widespread, affecting areas of up to several tens to hundreds of thousands km². Agriculture is the economic sector most impacted by tephra emissions during explosive volcanic activity, posing serious threats to agricultural activities and rural livelihoods. Crops are particularly vulnerable to tephra, with impacts ranging from reduced yields to total destruction. Although the detrimental effect of tephra on vegetation has long been recognised, our current understanding of crop vulnerability to tephra suffers from a significant deficit in knowledge. This situation is rooted in limited data availability and poor descriptions of the intertwined volcanic and non-volcanic factors dictating the level of tephra damage to crops. As a result, our capacity to inform appropriate risk reduction, management, and long-term recovery strategies in regions exposed to volcano-related hazards is limited. In this PhD research, we have identified the main impact mechanisms explaining crop production loss after exposure to tephra and their governing factors. We have also generated a new database that can underpin the development of quantitative tools for describing crop vulnerability to tephra. These results will aid in the development of more robust risk assessment methodologies for crops subjected to the tephra hazard., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Characterization of soil electromagnetic properties has always been an important task for hydrology, meteorology, environmental sciences, agriculture etc. In the meanwhile, airborne technology has been developed and applied to various applications. This thesis aimed to develop and analyse new ground-penetrating radar (GPR) techniques that are specifically designed for Unmanned Aerial Vehicles (UAV). The thesis involves radar antenna design and calibration, frequency sensitivity analyses based on the reflexion coefficient and full-wave inversion, numerical simulations using analytical Green’s functions and finite-difference time-domain (FDTD) methods, and validations with field measurements. The concept that drone-borne GPR and the full-wave inversion methods can be used for soil moisture and electrical conductivity mapping using drone was demonstrated. In particular, at relatively low frequencies, i.e., < 50 MHz, the soil surface reflexion coefficient becomes strongly sensitive to electrical conductivity and much less sensitive to permittivity. We extended the radar equation and its calibration to varying antenna pointing angles in both the E- and H-planes, which is of concern for UAV-GPR applications. Finally, we analysed the reflection problem for the trench-hill structures of the potato fields in order to map the root-zone soil moisture, e.g., to support irrigation practices. The outcomes of this thesis are useful in precision agriculture for sustainable production, by permitting real-time determination for precise and automatic irrigation. They enrich air-coupled GPR application avenues for soil surveys in terms of the root-zone electrical conductivity, by operating at intermediate frequencies between GPR and electromagnetic induction (EMI). They enrich remote sensing methods and applications of drone technology in the soil mapping aspect, by providing more information on the soil properties and giving soil maps with higher resolution and efficiency., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Sterile inflammation occurs when endogenous molecules termed damage-associated molecular patterns (DAMPs) are released into the extracellular environment and activate immune receptors to induce the secretion of pro-inflammatory cytokines. As this phenomenon contributes to the pathogenesis of many diseases such as ischemia-reperfusion injury, understanding how DAMPs are able to induce a pro-inflammatory response is of crucial importance for the development of new therapeutic strategies. Recently, human peroxiredoxin (PRDX) family proteins have been reported to act as DAMPs. However, the molecular mechanisms allowing PRDXs to induce a pro-inflammatory response remain to be clarified, starting from the early step of PRDX recognition (i.e. binding to receptors) to the late events triggered within the cell (i.e. cytokine secretion). In this PhD thesis, we used human PRDX2 and PRDX5 to investigate the role of (i) Toll-like receptor 4 (TLR4), one of the major innate immune receptors involved in pro-inflammatory responses, (ii) TLR4 accessory molecules MD-2 and CD14, and (iii) the redox state of PRDX cysteine residues, in the PRDX pro-inflammatory activity. To this end, we used a multidisciplinary approach combining biomolecular and biophysical techniques to gain insights into the binding properties of PRDX2 and PRDX5 towards TLR4 and its accessory molecules, as well as interleukin-8 secretion from cells exposed to PRDX2 and PRDX5. Using these approaches, we confirmed the role of TLR4 in the pro-inflammatory activity of PRDX2 and PRDX5 and further demonstrated that both PRDXs are able to interact directly with TLR4. Moreover, we showed that disulfide PRDX5 triggers potent pro-inflammatory response compared to reduced or hyperoxidized forms of the protein, and that the catalytic cysteine is required for the PRDX5 pro-inflammatory activity. We next observed that MD-2 is required for the TLR4-dependent cytokine-inducing ability of PRDX2 and PRDX5. In addition, we discovered th, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2022

Rhizomania is a major disease of sugar beet caused by Beet necrotic yellow vein virus (BNYVV), a benyvirus transmitted by the root-infecting plasmodiophorid protist Polymyxa betae. The obligate parasitic nature of plasmodiophorid organisms has long hampered efforts to obtain axenic cultures and complicated the sequencing of their entire genome. In this thesis, genomes of two P. betae isolates were, for the first time, assembled from distinct DNA samples using cutting-edge metagenomic techniques. The two nuclear genomes are very similar, each with ~10.2k protein-coding genes. Extending genomic comparisons to other plasmodiophorids, including mitochondrial sequences, revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae. Putative virulence factors found in P. betae are absent from other plasmodiophorids, and vice versa, revealing that they probably use distinct strategies to invade their hosts. A new protocol for the soil-free transmission of BNYVV to sugar beet by P. betae zoospores was developed and successfully applied to perform transcriptomic analysis of the tripartite interaction in rhizomania, using genetically characterized organisms. When nonviruliferous P. betae was inoculated in sugar beet, the protist implemented a strategy to circumvent plant defenses. The presence of BNYVV accelerated the development of P. betae, probably due to the action of the virus on plant cell walls and/or to its ability to suppress host RNA silencing. Moreover, BNYVV enhanced the induction of plant defenses and accelerated sporosori production. This earlier transition to the survival stage could either be due to the stress induced by plant defenses on P. betae or to a lack of resources or free root cells (not already containing protist structures) for further multiplication of P. betae., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Cannabis sativa L. is a promising species for non-food production on moderate heavy metal (HM)-contaminated farmland soils and considered as a potential crop for cleaning the soil from HM because of its high biomass production, its long root system and its capacity to absorb and accumulate HM. However, until now, “soil remediation” is usually considered independently of “soil production”, and there is an obvious lack of information regarding the possibility to conciliate phytomanagement and obtaining valuable marketable products. The global aim of the present thesis is to contribute to fil this gap, with specific attention to hemp fibres, the most economically valuable part of the plant. Using two different growing systems (nutrient solution or contaminated agricultural soil), we investigated the contaminant concentration and distribution in hemp raw material, hemp HM tolerance, and the impact of HM on fibre production and quality, considering for the first time industrial standards. We showed that C. sativa is suited for fibre production associated with HM management due to its extraction potential. However, this strategy should be limited to soils with a moderate content of HM, considering that high HM bioavailability negatively impacted plant growth and development. The management of moderately HM-contaminated soils with hemp can contribute to reduce the dispersion of HM in the environment through its high biomass yield and its important root system. Besides, HM impacted fibre elongation and thickening, but not their mechanical properties, and were mainly accumulated in trichomes rather than in fibres. Fibres could thus be used in special products like insulating material and cements, with a specific attention to the stability of these material regarding the erosion of the final product. To devise agricultural strategies aimed at improving crop yield, the effect of silicon (Si) on plants’ stress resistance was also considered. Overall, we demonstrated that the ad, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Aquaporins are channels facilitating water movements through biological membranes. In plants, they are involved in many essential processes (cellular homeostasis, tissue hydraulic...) and are key players of the response to environmental cues. While the varying expression patterns of aquaporin genes have been described across organs, developmental stages and stress conditions, the elucidation of the responsible regulation remains elusive. Hence, this work aimed to shed light on the expression variability of five plasma membrane aquaporin (PIP) genes in maize leaves, and its genetic causes, via eQTL (expression quantitative trait locus) mapping across a 252-hybrid diversity panel. The implemented genome-wide association study mapped many eQTLs, either close to, or distant from, the cognate PIP genes. A careful scrutiny of the results, including the evaluation of potential technical bias sources, strengthened the selection of eQTLs for further functional validation. Ultimately, two eQTLs associated with PIP2;5 expression variation were characterized. Genomic sequence comparison and in vivo reporter assay allowed attributing, at least partly, the local eQTL to a transposon-containing polymorphism in the PIP2;5 promoter. Further data, however, unveiled a more complex regulation depending on cell types, organs and environmental conditions that likely fine-tunes PIP2;5 expression in planta. The preliminary investigation on the candidate NAC24 transcription factor identified within a distant eQTL led to promising results, including the PIP2;5 transactivation in the presence of NAC24 in vivo. This work thus opened opportunities regarding the molecular elucidation of PIP gene regulation, and its possible integration into larger networks regulating physiological and stress-adaptation processes., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Nowadays, the demand of consumers for adopting new natural agents to protect against food-borne diseases like campylobacteriosis, salmonellosis or listeriosis has triggered the search for new bio-preservatives. Vietnam is known for its wealth of safe traditional fermented foods based on spontaneous fermentation. Interestingly, these products have surprisingly long shelf life, up to several years. The present study aimed to get more inside into the bacterial diversity of traditional Vietnamese fermented foods and to develop bio-preservative agents from GRAS (Generally Recognized as Safe) bacteria, for the control of foodborne pathogens. The composition of the microflora in traditional Vietnamese fermented foods was first exam-ined using a metagenomic approach. This analysis showed that LAB (Lactic Acid Bacteria), especially Lactobacillus spp., were predominant in all samples. Besides, other GRAS strains, such as members of the Bacillus subtilis group, were found with a noticeable abundance in samples of fermented meat, vegetables and marine products. Then, the antibacterial compounds from LAB and members of the B. subtilis group were screened against a panel of foodborne pathogens and characterized for their potential applica-tions. This screening selected one Lactobacillus brevis and eight Bacillus velezensis strains for their broad range antibacterial activities. The antibacterial compound from L. brevis strain HQV07 isolated from thit chua displayed activities against various bacteria, including the Gram-positive Listeria innocua, Bacillus cereus, Staphylococcus aureus and the Gram-negative Escherichia coli, Salmonella enterica, Yersinia enterocolitica and Campylobacter jeu-jeni. This antibacterial compound has the molecular weight of ca. 2.5 kDa and was shown to be sensitive to proteolytic enzymes and stable at 72oC for 15 min. Besides, bacilysin, a non-ribosomal peptide, was found in all Bacillus velezensis strains by using Ultra High Perfor-mance Liquid Chromat, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

The antimicrobial properties of silver nanoparticles (AgNPs) render them highly attractive for the food sector as they allowed the development of antimicrobial coating for appliances, tableware and kitchenware as well as the production of food packaging and containers reducing microbial development. Due to their increasing incorporation in products of the food sector, AgNPs are most probably ingested by consumers and pass through their gastro-intestinal tract (GIT) before, possibly, reaching systemic circulation and tissues. Some studies have already evidenced cellular damages caused by AgNPs in different cell lines. Since this toxicity is mediated by their physico-biochemical properties, the interaction of AgNPs with food and their passage through the GIT could alter their initial properties and consequently influence their behaviour upon digestion. The aim of this thesis consisted in the development of an in vitro method based on the incorporation of AgNPs in a standardised food matrix followed by the simulation of a pre-colonic digestion to study their behaviour in the GIT. The first part of this thesis focuses on the physico-biochemical properties of digested AgNPs and confirmed that they could reach the gut epithelium under nanometric form, although their properties are modified by food and gastro-intestinal fluids. In a second part, after an appropriate validation of the model, the alteration of AgNPs cytotoxicity after their passage in the GIT was evidenced by using a model representing the two major cell types of the gut epithelium. Altogether, this work revealed the need of taking the fate of nanomaterials in the GIT into account to perform accurate cytotoxicity testing as well as an appropriate risk assessment of ingested nanomaterials., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

The Sustainable Development Goals (SDGs) are a global initiative lead by the United Nations to achieve "a better and more sustainable future for all". Given the increasing impact of climate change on the available water resources over the past two decades, a particular attention is paid to water through SDG 6. The SDG-6 aims to "ensure availability and sustainable management of water and sanitation for all". This goal comes with a set of highly interconnected targets and indicators that are essential for its global and local implementation. Tunisia, as a member of the United Nations, adopted the framework of the SDGs with a particular interest in SDG 6 since Tunisia is considered as one of the highly water stressed countries in North Africa. Despite the growing need for a rapid, yet consistent, implementation of the goal in the country, very few scientific initiatives are working on monitoring the different indicators at the national scale using nationally-produced data. However, lower scale implementation and monitoring of SDG 6 indicators are essential to provide a consistent overview of the current state of water resources in the country. The current data infrastructure in Tunisia represents a major constraint, since the water-related information is poorly monitored and not accessible at the regional scale. This is due to the complex water institutional system, which is mostly dominated by the lack of coordination and communication between the different data providers. Nevertheless, over the past decade, participatory approaches for water monitoring have been getting more attention in many parts of the world, especially with the emergence of novel cost-effective smart technologies. Such participatory approaches are often referred to as Citizen Science (CS). With CS, citizens are involved in scientific activities, such as environmental monitoring, and they also can be a valuable part of decision making and policy formulation. Together with the generic available da, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

The Flemish beef sector faces growing economic uncertainty and societal criticisms. Agroecology is regularly proposed as an alternative development pathway, yet what this exactly means in this context is largely unexplored. This doctoral research aimed at investigating the relevance of agroecology to beef farming in Flanders. By gathering and analyzing data from a diverse group of Flemish beef farmers with both qualitative and quantitative methods, this dissertation renders agroecology as a practice more concrete conceptually in this context. The analysis of these farmers accounts also served to lay bare important ambiguities and inadequacies within agroecological thought with regard to the transformative potential of these agroecological practices, farmers, and the systems they construct. Out of this dialogue between agroecology and farmers thus emerged a more general societal reflection that advances contemporary ideas and practices to transform food systems, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Bacillus spp. offer a promising and sustainable alternative in crop protection. Both their direct antagonism towards pathogens as well as their indirect action by either eliciting systemic resistance or stimulating plant growth is mostly explained by the numerous bioactive compounds they produce. Our objective was to evaluate and understand how the B. subtilis 30B B6 can control early and late blight diseases on Solanaceae. Recent work reported the interest of 30B-B6 against potato late blight caused by Phytophthora infestans, an hemibiotrophic pathogen. This research aims to deepen knowledge on the effective biocontrol potential of this strain by performing further field trials and investigating its activity against potato early blight caused by the necrotrophic pathogen, Alternaria solani. Field experiments have proved that 30B-B6 can contribute to reducing the potato late blight pressure. Greenhouse experiments on tomato revealed that 30B-B6 also reduced (up to 76%) the disease pressure caused by A. solani, showing that 30B-B6 exhibits effective antagonistic properties against hemibiotrophic and necrotrophic pathogens. Bioassays performed on tomato plants also revealed the that the application of the bacterium on the root substrate led to reduce the disease severity to the same level as the foliar treatment. B. subtilis 30B-B6 is able to control the pathogen by direct antagonism and by stimulation of the plant defenses. This work gives a first insight into the molecular pathways involved in the induction of systemic resistance by 30B-B6 in tomato. We used RT qPCR and salicylic acid (SA) quantification to understand the action of 30B-B6 on plant defenses. We showed that the genes PR2b and WRKY1, coding for a glucosidase and a transcription factor involved in the expression of SA dependent genes, are overexpressed in plants displaying resistance to the pathogen after a treatment with the bacterium. The higher content of SA in these plants supports the involvement o, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Viruses are the most numerous species on earth. Some of them can be the cause of mild to severe diseases with potential deadly outcomes. Viral infection is initiated by the attachment of virus particles to the surface of target host cells. Understanding the molecular interactions taking place between virus particles and cell surface molecules is of fundamental interest for the development of new therapeutics interfering with virus attachment processes. Most of the insights gained on virus-cell interactions are currently obtained via ensemble molecular studies providing average responses of populations of virions. To unveil molecular details arising from biological variability, studies performed at the single virus particle-level could provide new valuable insights into virus attachment mechanisms. The aim of this PhD thesis is therefore to implement new tools to decipher the putative roles of viral surface glycoproteins upon attachment to cell surfaces at the single-virus particle level. This work involves the use and development of atomic force microscopy-based single-virus force spectroscopy (SVFS) to decipher the molecular mechanisms of herpesvirus attachment to cell surface glycosaminoglycans (GAGs). We investigated the attachment properties of single virions of Murid Herpesvirus-4 (MuHV-4) and Herpes Simplex Virus-1 (HSV-1) towards both purified GAGs grafted onto inert surfaces and GAGs on living cell surfaces. We observed that both glycoprotein gp150 (MuHV-4) and the mucin-like region of glycoprotein gC (HSV-1) play regulatory roles upon attachment of virions to GAGs, by regulating the multivalency of other viral glycoprotein-GAG interactions. We further deciphered the putative roles of two apparently redundant glycoproteins of MuHV-4: gH/gL and gp70. We showed that gH/gL provides a larger contribution to virus-GAG interactions than gp70 and that the gH/gL-GAG interactions have a higher inherent stability. The molecular insights gained by SVFS on the complex m, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

On average, increasing tree species diversity in forest stands results in higher productivity and stability of productivity, as well as in a larger range of ecosystem services; however, those effects are strongly context-dependent. In my PhD, I therefore explored some mechanisms possibly involved in species-mixing effects and looked at their dependency to spatial and temporal variations of environmental conditions. More specifically, I analyzed species-mixing effects on proxies of water and nutrient use, and on climate-growth relationships for Scots pine and European beech growing in pure and mixed-species stands (triplets) using a network of sites covering a large ecological gradient across Europe. This work was conducted along three axes. The first one aimed at analyzing the effects of species interactions on water related processes using wood carbon isotopic composition as an indicator of tree water use efficiency. I found that complementarity displayed a humped-shaped curve with maximal (positive) values for dry sites and close-to-zero values for extremely dry ones. In addition, species-mixing effects on non- or moderately constrained sites were strongly dependent on water- and possibly light-related species traits. No coherent species-mixing effects on drought resistance along the gradient was found for either species. The second axis aimed at analyzing pine and beech foliar nutrient composition in pure and mixed stands along a gradient of sites nutritional richness. Significant species-mixing effects on both foliar nutrient concentrations and stoichiometry were found. Interestingly, those effects tended to be higher on richer sites. Lastly, I analyzed the large-scale variability of species-mixing effects on average climate-growth relationships and drought resistance for pine and beech across Europe. The results highlighted the strong influence of regional climate on climate-growth relationship but coherent species-mixing effects were only found in case of over, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

In Europe, forests cover approximatively 35% of land area and offer a vast amount of goods and services: wood and non-wood production, biodiversity conservation, soil and water protection, carbon storage, recreation. For the last decades, the release of CO2 in the atmosphere and the lengthening of the vegetation period due to warmer conditions generally have had a positive impact on the forest productivity but, in the same time, the dryer conditions have also locally led to productivity decline and mortality events. Given the future climate projections, it is likely that these trends will accelerate in the future and have an impact on European forest state but local site conditions could modulate this impact. A promising approach to increase the forest resilience to future conditions is to favour uneven-aged structure and species mixture. Models able to simulate the response of structurally-complex stands to climate change are therefore crucial. In this project, I participated to the development of HETEROFOR, an individual-based and spatially explicit tree growth model through the integration of a phenological and a water cycle module, two processes key to assessing how climate change will affect forests. Using this model, I realised projections of the future forest productivity according to different climate models and scenarios with the objective of assessing how climate change will affect oak and beech tree growth in European temperate forests and how this response will be modulated by the local soil, stand and climate conditions. The results show that under the hypothesis of a constrained CO2 fertilizing effect, the forest productivity would increase on average in the temperate continental and mountainous regions but would decrease in the oceanic area due to higher hydraulic stress exceeding the effect of the longer vegetation period. When accounting for the CO2 fertilizing effect, a generalized increase in productivity was simulated. The climate, stand and soil, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Nuclear reactors waters are typically maintained in ultrapure state and are exposed to varying levels of radiation. Despite the extremely challenging conditions, microorganisms have been previously detected in these environments. The aim of this work was to investigate the bacterial communities in different waters of the BR2 nuclear reactor at SCK CEN, with a particular focus on the basin surrounding the reactor vessel. First, we investigated the viable microbial population in various water bodies using a cultivation-based approach. This yielded an extensive strain collection of 33 bacterial species. One of the isolated strains, Sphingomonas melonis, was shown to be somewhat radiation-resistant, as it survived a radiation dose of 2.1 kGy. Next, we characterized the long-term community dynamics in the basin through 16S rRNA amplicon sequencing. This resulted in the characterization of a diverse bacterial population displaying clear shifts in community profiles: cycles of operation were mostly dominated by an unclassified Gammaproteobacterium and Pelomonas, whereas Methylobacterium prevailed during shutdowns. Finally, we studied the functional characteristics of the microbial community in the basin through shotgun metagenomics. Several pathways with a role in cell function recovery after irradiation were more highly represented during shutdowns. Furthermore, two MAGs were almost entirely reconstructed from the metagenome, namely Bradyrhizobium sp. BTAi1 and Methylobacterium sp. UNC378MF. In conclusion, we managed to uncover a large bacterial diversity in various waters of the BR2, which were shown to harbor significant evolutionary adaptations allowing them to survive in these extremely challenging environments., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Bacillus cereus s.l. is soil dweller that gathers rode-shape Gram-positive, and spore forming bacteria. The group contains beneficial, non-pathogenic as well pathogenic species. From their natural environment, B. cereus contaminates food products and can cause two types of foodborne diseases: emetic and diarrhoeal syndromes. In 1998, a fatal diarrhoeal outbreak occurred in a nursing house in France. Bacillus cytotoxicus, a thermotolerant B. cereus, was isolated and shown to harbour cytK-1, a gene encoding the most cytotoxic variant of Cytotoxin K, one of the three prominent enterotoxins presumably responsible of the diarrhoeal syndrome. This thesis aimed at exploring the ecological niche of B. cytotoxicus, assessing its diversity and clarifying the role of CytK-1 toxin in B. cytotoxicus cytotoxicity. Our results support that B. cytotoxicus is rare in nature. Overall, 39 out of 339 (11,5%) food and environment samples were positive to B. cytotoxicus, with a high prevalence in potato flakes and potato derived products. From Malian foods though, B. cytotoxicus was also found in Millet flour for children and fish powder for the first time ever. A study case in a potato processing food-industry revealed that B. cytotoxicus and other thermotolerant B. cereus were positively selected by the industrial process. Band-based profiling (RAPD and plasmid profiling) of 57 strains showed six RAPD patterns and eleven plasmids profiles. SNPs computing revealed that strains with RAPD pattern A fitted in genomic clade C while those with pattern D clustered in clade D. Sole members of RAPD patterns E and F did not fit in any genomic clade. Inositol degradation and acetoin anabolism operons, and lactose uptake and utilisation coding genes were first ever reported in B. cytotoxicus. Prophages sequences and plasmid content played a role in genomic diversity the species. A mutant lacking in cytK-1 gene showed significantly decreased cytotoxicity. This indicates that CytK-1 is the main toxi, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Organogenesis is the phase of embryonic development leading to the formation of fully functional organs. It can be divided into two main processes: morphogenesis (acquisition of a shape and cellular organisation) and differentiation (acquisition of cellular function). The thyroid, a highly vascularised endocrine gland, derives from the endoderm and develops into its typical architecture (a multitude of tightly packed independent spherical follicular units) starting from a 3D mass of epithelial thyroid progenitors. Follicular organisation is unique and essential for thyroid function, i.e. thyroid hormone (T3 and T4) production. Previous in vivo studies showed that endothelial cells , besides their nutritive function, play a central role in thyroid gland morphogenesis. However, the precise mechanisms and biological parameters controlling the organisation of the thyroid epithelial progenitors into a multitude of singlelayered thyroid follicles remain unknown. Animal experimentation to improve our knowledge of organogenesis is time- and money-consuming and has clear limitations. Here, we developed and used a 2-D vertex model of thyroid growth, angiogenesis and folliculogenesis, within the open-source Chaste framework. Our in silico model, based on initial in vivo images, correctly simulates the differential growth and proliferation of (central and peripheral) epithelial progenitors, as well as the morphogen-driven migration of endothelial cells, consistent with our experimental data. We show that endothelial invasion, associated with changes in epithelial cell adhesion, are key in driving the fission of the 3D epithelial mass into independent prefollicular units. We also found that endothelial cells abundance and proximity to epithelial cells could induce their polarisation and subsequent opening of a cavity in the centre of the follicle. Our study illustrates how constant dialogue between theoretical and experimental approaches helped us better understand the role of c, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

This Ph.D. aims at clarifying the future trajectories of the Walloon dairy sector, based on a study of the strategies and constraints of dairy cooperatives as collective agents. From a systemic perspective, the Ph.D. considers, on the one hand, the dairy cooperatives’ strategies within a given context, and the impact of that context on their strategies. On the other hand, dairy cooperatives are approached as structures of collective action, interplaying in terms of governance with its farmers-members. The focus lies on an in-depth understanding of the factors enabling or disabling certain trajectories, in particular the trajectories of product diversification (productions other than drinking milk, milk powder, butter; productions relying on a definition of milk quality broader than that of industrial standard raw material). The Ph.D. consists of four parts: a historical investigation, an analysis of coordination models in the dairy value chain, a study of the co-existence of cooperative models today, and a zoom on how farmers relate to the dairy value chain. The Ph.D. uncovers that different models of horizontal and vertical coordination may co-exist, beyond the classic model of vertical integration, and that a combination of different models of coordination may support a transition towards a diversification of dairy productions at regional scale. The Ph.D. also highlights a structural tension between the short-term interests of the dairy farmers as milk suppliers and their long-term interests as cooperative members. This tension can influence the strategic choices of cooperatives, which implies that attention must be paid on how dairy farmers relate to collective action., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

In temperate regions, climate change is leading to more frequent droughts and higher average temperatures, impacting all ecosystems. Most flowering plants in temperate zones depend on insect pollinators for their reproduction. Insect pollinators collect floral resources, pollen and nectar, which they sometimes rely exclusively on it for food. Plants attract pollinators through floral signals (flower size, quantity of floral resources, etc.). If these signals are altered, the mutualistic relationship between plants and pollinators can be compromised. My thesis aims to investigate climate change-induced changes in floral signals and their potential impact on pollinator behaviour. Plants, during their flowering period, were subjected to combined stresses (increased temperatures and drought) under controlled conditions. Collectively, the results of the research conducted in this thesis confirm that these stresses negatively impact the floral signals and resources of the plants. When pollinators were exposed to a binary choice between 'unstressed' and 'stressed' flowers, 75% of them chose the unstressed flowers. These results indicate that the change in floral signals of stressed plants is perceived by insects, which may compromise pollinator attractiveness and potentially plant reproductive success., Dans les régions tempérées, les changements climatiques induisent des sécheresses plus fréquentes ainsi qu’une température moyenne plus élevée, impactant l’ensemble des écosystèmes. La majorité des plantes en zone tempérée dépendent des insectes pollinisateurs pour assurer leur reproduction. Les pollinisateurs, en butinant, récoltent des ressources florales, du pollen et du nectar, dont ils dépendent parfois exclusivement pour leur alimentation. Les plantes attirent les pollinisateurs grâce à des signaux floraux (taille de la fleur, quantité de ressources florales, etc.). Si ces signaux sont modifiés, la relation mutualiste entre les plantes et les pollinisateurs peut être compromise. Ma thèse vise à étudier les modifications des signaux floraux induites par les changements climatiques ainsi que les répercussions potentielles sur le comportement des pollinisateurs. Les plantes, durant leur période de floraison, ont été soumises à des stress combinés (hausse de températures et sécheresse) en conditions contrôlées. Collectivement, les résultats des recherches menées dans le cadre de cette thèse confirment que ces stress impactent négativement les signaux floraux des plantes. Quand les pollinisateurs ont été soumis à un choix binaire entre des fleurs « non stressées » et « stressées », 75% d’entre eux se sont orientés vers des fleurs non stressées. Ces résultats indiquent que la modification des signaux floraux des plantes stressées est perceptible par les insectes, ce qui peut compromettre l'attrait des pollinisateurs et potentiellement le succès reproducteur des plantes., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Following the global economic crisis in the 1980s, Côte d’Ivoire adopted liberalisation reform within its agricultural sector. Although this shift in policy has led to notable achievements, evidence of its effects on improving farmers’ incomes and enhancing growth is still mixed. Three decades later, the living conditions of rural agricultural households have not improved and their degree of vulnerability has further increased. In this context, this research sheds light on the impacts of the liberalisation reform on producer price dynamics, supply and agricultural services provision to farmers in C^ote d’Ivoire. In particular, it focuses on three major commodities, namely Rubber, Cocoa, and Palm Oil, and addresses multiple questions using time series econometrics as well as game theory models. The first chapter analyses the transmission of rubber world prices to the domestic market. It highlights the link between world price and domestic Ivorian producer prices and tests the presence of asymmetry in the transmission process. The second chapter focuses on the cocoa producer price and supply responses to world price shock after the liberalisation reforms with a comparison to the neighbouring Ghana which has not fully liberalized its cocoa sub-sector. The third chapter presents a theoretical assessment of the impact of competition between processors on the provision of agricultural services to farmers. The key findings of this research will help to formulate policies to enhance the competitiveness of the agricultural export sector and improve farmers’ incomes., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2021

Hydrological systems seem simple, "everything flows", but prove to be even more complex when one tries to differentiate and characterize flows in detail. Hydrology has thus developed a plurality of models that testify to the complexity of hydrological systems and the variety of their causal representations, from the simplest to the most sophisticated. Beyond a subjective complexity linked to our difficulty in understanding or our attention to detail, hydrological systems also present an intrinsic complexity. These include the nonlinearity of processes and interactions between variables, the number of variables in the system, or dimension, and how they are organized to further simplify or complicate the system's dynamics. The thesis addresses these aspects of hydrological complexity. An epistemological and historical analysis of the concept of causality explores the human understanding of hydrological systems. Based on empirical approaches applied to the limestone karstic system of the Lhomme at Rochefort in Belgium, the thesis then studies methods to analyze the nonlinearity of the Lhomme river recession and associate it with the geomorphological complexity of the watershed. The thesis also handles the discrimination of dominant dynamic behaviors in the hydrological continuum of the Rochefort caves subsurface based on an electrical resistivity model of the subsurface and clustering methods grouping time-series according to their similarity. Finally, the study maps the Rochefort Caves system's organization by detecting causal interactions between several environmental data - gravity, the dynamics of subsurface resistivity, and percolations measured in the caves - using time-series analysis and causal inference methods., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2020

Grilled pork (GP), smoked fish (SF) and smoked-dried fish (SDF) are popular foods in Benin. They are processed by small cottage industries for direct consumption at household level, as street food, or are intended for local and sub-regional markets. Although playing important socio-economic and nutritional roles, the conditions under which these foods are processed make their safety questionable. This study aimed to assess and improve their microbiological quality. This work first consisted in a survey from processors with the aim to review the local knowledge on technologies of production of GP, SF and SDF. Practices of processing raw pork into GP and fresh fish into SF and SDF, the storage conditions applied, and the quality attributes of the end products were documented. The microbiological quality of GP, SF and SDF as sold to consumers were then assessed through samples collected from various processors. Out of 60 samples investigated, 26 (43%) were not compliant with acceptable limits recommended by the Health Protection Agency (HPA) for Aerobic mesophilic bacteria (AMB), Enterobacteriaceae, Escherichia coli, Bacillus cereus and Clostridium perfringens. Furthermore, microbial density of moulds up to 6 Log10 CFU g-1 was recorded in some samples. No sample contained Salmonella spp., Staphylococcus aureus or Listeria monocytogenes. A metagenomics approach was also used to explore the bacterial diversity of SF and SDF. The 48 SF and SDF samples randomly collected displayed substantial diversity profiles. Through a follow-up of processing trials, performed by experienced processors, several quality-compromising practices related to processors, raw material, processing methods and equipment were identified. Based on these results, improved processing practices adapted to the cottage industries of pork grilling and fish smoking were proposed and implemented by the processors, and the safety of the end products was assessed. 100% of samples exhibited AMB loads ranged f, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2020

Sahelian woody vegetation has been the topic of many researches since the great drought that struck the Sahel in the 1970s-1980s. However, there is currently no consensus about the long-term trends of these savannas as observations sometimes seem contradictory according to the indicators used. Moreover, the observed trends often lack an understanding of the consequences on ecosystem functioning and subsequently on the provision of ecosystem services (ES), even if a decrease in ES is often assumed. As the inhabitants of the sylvo-pastoral zone of Senegal rely on these ES in their daily life, it is crucial to be able to predict the woody vegetation response to the current pressures acting on these ecosystems. In this research, we investigate the long-term trends of woody vegetation in order to discuss its persistence and its effects on two ecosystem functions (primary productivity and biogeochemical cycles) when facing three types of disturbances (drought, fire and grazing). This vegetation is examined from 1965 to 2018 using different indicators of the vegetation state and persistence, computed at several spatial scales and derived from multiple datasets (field inventory, remote sensing and literature). We first studied the spatial differentiation of the current woody vegetation according to the topography. Second, we evaluated changes since 1965 onward in terms of specific composition, density and woody cover. Third, we transposed the different indicators from the first two parts into a functional level of the woody communities, focusing on the vegetation response to pressure and effects on ecosystem. Based on this functional approach, we suggest some avenues for a potential management of this zone, in order to maintain the sylvo-pastoralism as land use., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2020

Carbohydrate active enzymes play an important role in biorefining. They are key players in the deconstruction of polysaccharides, with applications for the production of bio-molecules and renewable fuels from lignocellulosic biomass. In the context of bioprospecting for such new enzymes, the aim of this PhD thesis was to characterize the carbohydrate hydrolytic potential of lignocellulose-degrading microbiomes. Using metagenomics, metatranscriptomics and downstream bioinformatic analyses, I investigated the polysaccharide deconstruction potential of bacteria extracted from anaerobic bioreactors fed with sugar beet pulp, as well as from the gut of termites exposed to a miscanthus diet. I enlightened the genomic redundancy of the carbohydrate hydrolysis function of the anaerobic bioreactor microbiome, i.e. the metagenomic potential was maintained while the operational conditions (pH) and composition of the bacterial community evolved. In the case of the termite gut microbiome exposed to miscanthus, an up regulation of carbohydrate active enzymes involved in lignocellulosic biomass deconstruction was observed. With the intention of confirming the in-silico predictions of the substrate specificity of selected carbohydrate active enzymes, I developed a complete in-vitro workflow, from DNA isolation to heterologous expression of the proteins and activity detection. This work led to the discovery of new carbohydrate active enzymes and related gene clusters, which bring additional knowledge towards the strategy employed by bacteria to deconstruct lignocellulosic biomass. Additionally, these nature-optimised enzymatic cocktails might be mimicked and new specific enzymes be introduced in the precision biorefining pre-treatments of lignocellulosic biomass., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2020

Drought is probably one of the biggest single threat from climate change which impacts are global, threatening particularly crop production. There is an urge in implementing sustainable agricultural practices in order to maintain/optimize crop production under drought conditions. AM fungi are soil microorganisms that establish symbiosis with more than 70% of land plants and whose role in mitigating the effects of drought on plants has been demonstrated in numerous studies. Optimization of plant-AM fungal association requires deeper investigation on the impact of decreasing water availabilities on these soil microorganisms and better knowledge on the role of these root symbionts in adaptation of plants to drought. In this thesis, we first investigated the effects of decreasing water availability on the life cycle, and on Pi uptake and transport capacity of AM fungi under strict in vitro culture conditions. Polyethylene glycol was used to decrease the water potential (reflecting water availability) of the growth medium. Germination and germ tube length of various AM fungal strains were affected differently and spores production, hyphal development and Pi uptake of the extraradical mycelium of the model fungus R. irregularis MUCL 41833 were impacted. Secondly, we evaluated if R. irregularis MUCL 41833 could still benefit plant despite an impact of decreased water availability on its biology. The effects of the fungus on Pi mobilization and leaf gas exchange parameters of maize plants grown in a semi-hydroponic cultivation system was assessed during recovery from drought. During recovery, the mycorrhizal plants took up Pi faster than the non-mycorrhizal ones, although both plants had similar root biomass and unrestricted access to Pi. The AM fungus also improved the instantaneous water use efficiency through a decrease of transpiration during recovery, possibly resulting in faster rehydration of the plants. In conclusion, AM fungi may behave differently under drought st, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2020

The continental cycle of silicon (Si) relies on the Si soil-to-plant cycle where the primary source of Si for plants is the reserve of soil weatherable lithogenic silicates (LSi). LSi weathering releases dissolved Si (DSi), which may follow four routes: formation of pedogenic silicates (PSi), adsorption on oxide surfaces, leaching to watersheds, uptake by plants that form silica bodies named phytoliths (PhSi). Within plant debris, Si returns to soil where phytoliths dissolve to provide plant available DSi. DSi from soil to plant and back to soil for plant uptake defines the biological Si feedback loop of the terrestrial cycle of Si. In croplands, harvesting and exportation of plant residues disrupt this loop, and aggravate natural soil desilication. Pyrolysis of phytolithic biomass from monocot residues produces Si-rich biochar which, when applied to soil, is a promising and environmentally friendly technique challenging desilication. Our scientific question is how to enhance the biological Si feedback loop in agroecosystems, given the many benefits of Si in plants. In a first step, we set up a soil-plant experimental design controlling PhSi supply through biochar and LSi supply through dosed additions of weatherable LSi minerals to a soil free of them, hence simulating a soil weathering gradient. The contribution of supplied phytoliths to Si accumulation in rice increased from 26% to 80% with increasing soil weathering stage, i.e. decreasing total reserve in bases from TRB 405 to 5 cmolc kg-1. LSi dissolution contributed to 7-14% of allophanic PSi synthesis, but to less than 1% of plant PhSi. Allophane rapidly formed from LSi dissolution at a maximum rate of 0.85 g kg-1 day-1. The increase in rice plant accumulation of Si enhanced photosynthetic activity, water uptake and transpiration, stomatal conductance, plant biomass and grain yield. In a second step, we study the impact of soil properties and processes upon the mobility of Si in the soilplant system. Our resu, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2019

Pospiviroids are plant pathogens, composed only of infectious RNA molecules. They are both latent on many ornamentals and harmful for cultivated plant species like tomato, potato, sweet pepper, citrus or chrysanthemum. Throughout the world, these pathogens cause sporadic outbreaks on susceptible crops, while they often remain undetected although widespread on ornamentals. In the EU, no official detection methods have yet been recognized for the detection of pospiviroids. There is also a lack of publicly available comparisons of existing methods. A new generic detection method based on reverse transcription polymerase chain reaction has been developed and validated according to the international standard ISO/IEC 17025. To assess this new method with already existing ones, an inter-laboratory comparison was organized at the EU level. In a second step, High-Throughput Sequencing, which arises as the next generation technology in plant disease diagnosis, was used to characterize the pospiviroid Citrus exocortis viroid-tomato pathosystem. In-depth analysis of generated sequences coupled with innovative bioinformatic analyses allowed for gaining insights into the molecular interactions between pospiviroids and their hosts. This new perspective provides a coherent answer to questions regarding viroid degradation, cell-to-cell trafficking, symptom expression and, consequently, to pending questions concerning viroid phytosanitary risk management. Moreover, from these analyses, emerging hypotheses allowing understanding the activation of plant innate immunity and systemic acquired resistance by these non-coding RNAs are proposed. Together with the possible interaction of RNAi in these processes, such hypotheses offer both new paths of research regarding these key phenomena of plant defense as well as new hope for the sustainable management of viruses and viroids in crops., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2019

Chemical weathering of subaerial volcanic rocks influences the chemical composition of rivers, lakes and soils where they have been deposited and/or transported. In the case of basaltic rocks, it also contributes significantly to the consumption of atmospheric CO2. However, the rates at which these rocks, which are characterised by various degrees of crystallinity and silica contents, dissolve upon contact with water are still not well described. The principal aim of this PhD study was to advance our understanding of this issue. Through laboratory experiments carried out with a home-built fluidized bed reactor, we provide new insights into the dissolution rates of volcanic rocks differing in composition and crystallinity. The main study findings are: (a) polycrystalline rocks dissolve incongruently, leaving a residual silica/aluminium-rich layer at the surface of the weathered material; (b) polycrystalline rocks dissolve at faster rates than their synthetic glassy counterparts, and the difference is more pronounced for rocks with higher silica contents; and (c) the dissolution rates of intermediate and silicic volcanic rocks can be approximated based on the dissolution kinetics of their major constituents, i.e. silicate glass and plagioclases ± pyroxenes. In addition to the experimental work, we modelled the weathering of a continent-size silicic tephra deposit over multimillennial timescales. Such deposits are typically emplaced by so-called supereruptions, for example, Yellowstone 0.64 Ma ago. The impact that these deposits may have on the geochemical fluxes of silicon and cations and atmospheric CO2 consumption over millennial timescales is not known. Using a mechanistic model (WITCH), we predict that the weathering of supereruption’s silicic tephra deposit can strongly enhance the continental flux of dissolved silicon to the ocean for several thousands of years. However, its effect on the concentration of atmospheric CO2 is minor, which is in contrast with the p, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2019

The immobilization of proteins to impart specific functions to surfaces is topical for chemical engineering, healthcare and diagnosis. Layer-by-Layer (LbL) self-assembly is one of the most used method to immobilize macromolecules on surfaces. However, when it comes to proteins, the promises of versatility, simplicity and universality that the LbL approach holds are unmet due to the heterogeneity of protein properties. This thesis aims at demonstrating that protein surface properties can be standardized via their complexation with polyelectrolytes (PEs), and that the resulting protein-polyelectrolyte complexes (PPCs) can be used as building blocks for LbL assembly. The results show that using PPCs, LbL assembly becomes independent of the protein electrical properties. In particular conditions, proteins from PPCs serve as a sacrificial element to build layers with specific properties. When compared to the LbL assembly of bare proteins, the PPCs-based method is shown to maintain a higher protein bioactivity and to immobilize larger protein amounts, which results in a higher total bioactivity. Finally, the method is translated to the creation of a dressing on which an antimicrobial peptide is immobilized thanks to the use of PPCs. The LbL assembly of PPCs thus holds much promises in terms of universality. It also allows to create new functionality and structures at interfaces, which will be beneficial for the design of drug delivery systems, biomaterials and sensors., (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2019

Alkylated resorcinols are important as antioxidant and widely used in the pharmaceutical and fine chemical industries. 4-tert-butylresorcinol is used as active component in the treatment of skin diseases and as colour developer. Resorcinol alkylation to 4-tert-butylresorcinol is an electrophilic aromatic substitution, traditionally carried out in homogeneous phase using strong Brønsted acids (e. g., H2SO4). The increasing environmental concern raised the issue of developing sustainable alternatives. The use of heterogeneous solid catalysts would reduce the amount of wastes produced since they can be easily separated from the reaction mixture by filtration. However, despite the important role of alkylated dihydroxybenzenes in the chemical industry, only few works involving the use of heterogeneous catalysts have been carried out in the last years. Even though resorcinol conversion was kept high (up to 99%) the selectivity to 4-tert-butylresorcinol were low, because of the formation of the di-alkylated product 4,6-di-tert-butylresorcinol. In addition, previous works have missed to address attention to the reaction mechanism at the catalyst surface. Further, the impact of the catalyst surface chemistry on the reaction was not investigated enough. In this context, this research project aims at answering the question: how to obtain 4-tert-butylresorcinol with good resorcinol conversion and high selectivity in a clean way? The resorcinol alkylation reaction mechanism and the catalyst surface chemistry are at the core of this research. Keggin phosphotungstic acid (HPW) was chosen as active phase to catalyse the resorcinol tert-butylation. To be used in a polar liquid environment, it was heterogenized by immobilization using the hydrolytic sol-gel method following two different approaches: the not-templated synthesis and the templated synthesis using surfactants. In the first group of catalysts, obtained with the not-templated approach, different supports (SiO2, TiO2 and Zr, (AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2019