37 research outputs found
Reverse genetic tools for exploring the plant-vector-virus pathosystems of beet black scorch virus and beet soil-borne virus
No full textSugar beet (Beta vulgaris) is threatened by several viral diseases amongst which the Rhizomania is the most devastating. This pathology is caused by Beet necrotic yellow vein virus (BNYVV), a multipartite RNA virus that is transmitted by the soil-borne plasmodiophorid Polymyxa betae. In diseased plants, BNYVV is frequently found in co-infection with other viruses such as Beet soil-borne mosaic virus, Beet soil-borne virus (BSBV), Beet virus Q and Beet black scorch virus (BBSV) as well as its associated satellite RNA (satRNA). These viruses have been relatively less studied in comparison with BNYVV, raising concerns regarding their impact on sugar beet. In particular, this thesis aims to shed light on the pathogenicity of two of those viruses: BSBV and BBSV. To this end, agroinfectious clones (shortly agroclones) were constructed for both viruses, allowing rapid plant inoculation via delivery by Agrobacterium tumefaciens. Such agroclones for both pathogens were efficiently used to demonstrate viral infections of two model plant species, namely Beta macrocarpa and Nicotiana benthamiana. In addition, infection was evidenced on sugar beet following mechanical inoculation by agroinfected material, allowing for the first time to show a symptomatic response from this host for viral cDNA clones of BSBV and BBSV. Eventually, transmission assays via zoosporic vectors were successfully carried out in order to validate a complete viral cycle. Indeed, BBSV and its satRNA were efficiently transmitted by zoospores of the fungus Olpidium virulentus that was originally recovered from infected soils. As far as BSBV is concerned, proof of transmission was given using resting spores of the P. betae strain A-2641. Altogether, the obtained results confirm that the developed agroclones are efficient tools for reverse genetics studies, paving the way for exploring the pathosystems of BSBV and BBSV, their sugar beet host and their respective vectors.(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 202
The wheat microbiome and its associated Pseudomonas
No full textIn the quest for sustainable agriculture, this thesis examines the role of biological control agents (BCAs), focusing on beneficial Pseudomonas within the cereal phytobiome. Our research began with the isolation and in vitro characterization of various Pseudomonas strains, revealing an unexpected abundance of P. sivasensis across all tested field locations and plant compartments. This led to the discovery of a new species closely related to P. sivasensis, designated P. arvensis sp. nov. P. sivasensis strain CF10PS3 stood out for its biocontrol potential and plant colonization capabilities. A novel qPCR probe protocol was developed to specifically detect and quantify the CF10PS3 strain, distinguishing it from naturally occurring counterparts. Strain CF10PS3 was sprayed onto wheat leaves in the field to monitor its persistence in the phyllosphere and assess its impact on existing microbial communities through a newly developed bioinformatic pipeline for species-level metagenomic evaluation. The study explored the ecological effects of introducing CF10PS3, evaluating its colonization efficiency, impact on native microbiota, and its role in modifying microbial community structures crucial for plant health. Our findings indicate that the strain CF10PS3 dynamically affects the phyllospheric microbial landscape, initially causing detriment to many species before shifting to a more balanced interaction, eventually promoting several species. These results underscore the capability of BCAs like strain CF10PS3 to act as precise microbiome modifiers, selectively enhancing beneficial microbial interactions without broadly altering overall community structure. This study advances our understanding of microbial dynamics in the phyllosphere and highlights the importance of integrating microbial management strategies into sustainable crop cultivation practices.(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 202
Regulation of water flow in the soil-root domain. New tools and methods
No full textWater flow in the soil-plant-atmosphere continuum is controlled by a handful of key features. On the plant side, the leaf stomatal conductance controls the total amount of water transpired while the root hydraulic properties defines the distribution of uptake sites in the soil domain. On the soil side, the soil hydraulic properties and the 3D distribution of water define the quantity of water available to the plant. The explicit integration of these factors is required to decrypt their quantitative influence in the uptake process at the plant scale.
In this work, different tools were developed to facilitate the observation and analysis of water flows in the SPAC. Firstly, a new root image analysis software, SmartRoot, was created to enable a quantitative analysis of root system architecture. Secondly, the creation of an experimental platform made possible the parallel monitoring of soil water content and root architecture of 20 plants. Finally, the implementation of a new functional-structural plant model, PlaNet-Maize, allowed the simulation of water flow regulation at the plant level with a resolution down to the organ. Using these new tools, the quantitative influence of several root features on the water uptake processes was evaluated. Firstly, deep-rooted plants were shown to ensure a better distribution of the water content decrease in the soil profile. Secondly, the regulation of root axial and radial hydraulic properties were shown to ensure a fine regulation of the flow in response to changes in the soil environment.
In conclusion, the successful development of new tools and methods allowed a more detailed analysis of the influence of several plant features in the water uptake process.(AGRO 3) -- UCL, 201
Linking soil hydraulic properties to structure indicators : experiments and modelling
No full textSoil hydraulic properties are needed for modelling below-ground water flow and solute movements. They are very variable in space and time and across scales and their characterisation is tedious. Pedotransfer functions (PTF) are tools developed to predict hydraulic properties from more readily available information. This thesis provides PTF predicting the parameters of a closed-form model of the soil hydraulic conductivity and moisture retention curves based on the soil texture, bulk density and organic carbon content. These PTF show their limits very close to saturation because the soil structure is not well apprehended by these indicators. With the aim of developing PTF considering the soil macroporosity, soils of homogeneous texture but contrasted structure (silt loam) are studied with a multistep outflow system and with fine resolution moisture retention measurements. It is first shown that the choice of the model has more impact than the spatial variability on extrapolation results and that, even with very good fitting performances, the prediction uncertainty can be very large. Assuming that land cover and horizon depth control the root architecture, the soil biological activity and land management practices, their impact on close to saturation hydraulic properties of silt loam soils is investigated. Results suggest that land cover should be included into the next generation of PTF. It is also shown that the presence of macropore is generalised in these soils. Finally, hydraulic properties of tropical soils derived from volcanic ashes are successfully linked with pedo-chemical and morphological indicators determined on exactly the same sample as the hydraulic measurements. Future use of this combination of information for developing PTF for tropical soils is therefore advised.(AGRO 3) -- UCL, 201
Mapping and source identification of groundwater pollution by nitrate : theory and application to the Brusselian sand groundwater body
No full textThis thesis aimed to improve our understanding of groundwater pollution by nitrate at the regional scale of the Brusselian sand groundwater body (Belgium). Despite all the nitrate reduction actions that were undertaken to meet European directives, this study area still presents one of the highest groundwater nitrate concentrations of the Walloon Region. Further assessing the pollution levels of groundwater and identifying the contamination sources are therefore needed for designing sustainable water management strategies.
Our first main objective was to assess groundwater contamination at the regional scale by mapping the nitrate concentrations. The locations where groundwater quality properties were measured are scarce and sparsely distributed over space. We therefore used a data fusion method in order to improve the mapping quality of groundwater nitrate concentrations in areas located far away from monitoring stations.
The transfer time of nitrate to the aquifer is one of the reasons that could explain the lack of improvement in water quality. We estimated the travel time of percolating water through the vadose zone.
Our second main objective was to identify sources of groundwater nitrate pollution in the study area. Two statistical methods were used to link the measured nitrate concentrations with land and land use attributes. The isotopic signature of groundwater nitrate allowed to identify the source of pollution observed in some monitoring stations, and gave insight about processes affecting the contamination.(AGRO 3) -- UCL, 200
Full genome sequence of a new polymycovirus infecting Fusarium redolens
No full textBy screening a collection of Fusarium spp. for the presence of dsRNA, the Fusarium redolens strain A63-1 was found harboring a pattern of multiple dsRNA bands when analyzed by agarose gel electrophoresis. Using NextSeq Illumina sequencing, the full sequences of eight dsRNA molecules were determined, compared to databases, and gathered into a new viral genome. This novel virus shares similarities with mycoviruses that were recently grouped in the proposed family “Polymycoviridae”. Hence, the name “Fusarium redolens polymycovirus 1” is proposed for this virus. Each viral dsRNA contains only one ORF, except dsRNA 7, which has an additional one. Based on amino acid sequence similarities, the functions of the proteins encoded by dsRNA 1–4 can be hypothesized. On the other hand, the putative proteins encoded by dsRNA 5–8 exhibit no relevant homology to known proteins. In this report, the full genome sequence of this new virus is presented along with a primary bioinformatics analysis
Monitoring the Persistence of Pseudomonas sivasensis Strain CF10PS3 in Cereal Fields
No full textABSTRACT The persistence and efficacy of biocontrol agents in agricultural fields are crucial for sustainable crop production. In this study, we investigated the persistence of the introduced bacterial strain Pseudomonas sivasensis CF10PS3 in the wheat phyllosphere using a novel qPCR probe protocol. The CF10PS3 strain, known for its in vitro biocontrol properties against wheat pathogens, was applied through foliar spray, and its persistence was monitored over 7 weeks. Our qPCR assays, designed to specifically detect CF10PS3, distinguished it from naturally occurring P. sivasensis strains, providing precise insights into its dynamics in the field. The experimental results indicated that CF10PS3 was already present on the wheat leaves before its application, suggesting its natural adaptation to the foliar environment. Following initial application, a significant increase in CF10PS3 was observed, though subsequent environmental factors such as rain and wind might have caused notable fluctuations in its population. Despite these variations, the introduced strain showed considerable persistence, with population levels significantly higher than those in untreated plots by the end of the study period. This research underscores the importance of understanding bacteria dynamics in the field, highlighting the influence of environmental conditions on their efficacy. The use of specific qPCR probes proved effective in monitoring introduced strains, offering valuable insights for optimizing biocontrol agent application strategies. Our findings contribute to the development of robust biocontrol methods, promoting sustainable agricultural practices and enhancing crop protection
Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela
No full textBegomoviruses are one of the major groups of plant viruses with an important economic impact on crop production in tropical and subtropical regions. The global spread of its polyphagous vector, the whitefly Bemisia tabaci, has contributed to the emergence and diversification of species within this genus. In this study, we found a putative novel begomovirus infecting tomato plants in Venezuela without a cognate DNA-B component. This begomovirus was genetically characterized and compared with related species. Furthermore, its infectivity was demonstrated by agroinoculation of infectious clones in tomato (Solanum lycopersicum) and Nicotiana benthamiana plants. The name Tomato twisted leaf virus (ToTLV) is proposed. ToTLV showed the typical genome organization of the DNA-A component of New World bipartite begomoviruses. However, the single DNA component of ToTLV was able to develop systemic infection in tomato and N. benthamiana plants, suggesting a monopartite nature of its genome. Interestingly, an additional open reading frame ORF was observed in ToTLV encompassing the intergenic region and the coat protein gene, which is not present in other closely related begomoviruses. A putative transcript from this region was amplified by strand-specific reverse transcription-PCR. Along with recent studies, our results showed that the diversity of monopartite begomoviruses from the New World is greater than previously thought
Overland flow connectivity : theory and application at the interrill scale
No full textTo predict the hydrological response of a hillslope to a rainfall event, the spatial configuration of soil roughness needs to be taken into account. Quantitative expressions of hydrological connectivity based on topography may improve the prediction of overland flow propagation, especially if the connectivity concept is applied at the subgrid scale of current hillslope models, which corresponds to the interrill scale.
Our first objective was to measure the effect of micro-topography on overland flow. Some of the water is stored in depressions (depression storage) and some is temporarily stored in the flowing water layer (surface detention). To measure those storages, we used a new molding technique that reproduced realistic but waterproof soil surfaces, which were subjected to artificial runoff. The evolution of both storages following rainfall was related to the cumulative rainfall erosivity value.
Our second objective was to find runoff-relevant connectivity properties of micro-topography. Based on numerical runoff experiments, we found that, among a number of existing structural connectivity indices and a proposed new functional connectivity index (namely the Relative Surface Connection function), the RSC function was the most robust and directly linkable to the runoff dynamics.
Our last objective was to introduce the connectivity properties captured by the RSC function at the subgrid (interrill) scale in distributed hydrological models. A corrective procedure was proposed to combine both surface detention and depression storage dynamics. It allows mimicking the hydraulic behavior of small plots where the effect of the micro-topography is characterized by few (1 or 2) effective parameters implementable in hillslope models.(AGRO 3) -- UCL, 201
