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Influence of biotic and abiotic factors on microbe-induced chemical defences in the "Solanum" clade
No full textDoctoral thesis submitted to satisfy the requirements for the Degree of Doctor ès Sciences
After acceptance by the Thesis Committee Jury
Prof. Dr. Sergio Rasmann Thesis director
Prof. Dr. Theodoor Turlings Internal rapporteur
Prof. Dr. Nicole M. van Dam External rapporteur
Dr. Emmanuel Defossez Examinator
Dr. Hanna Nomoto Examinator
Publicly defended on October 27th 2023Plant-associated soil-dwelling microbes, including bacterial and fungi, can greatly facilitate plant mineral nutrition, increase plant tolerance to abiotic stresses such as drought and salinity, as well as induce resistance to biotic stresses like plant pathogens and herbivorous insects. Therefore, using Microbe in agro-ecosystems appears more and more as a promising opportunity to reduce the use of pesticides while improving crop resilience. However, this needs to be further studied. Specifically, the use of microbes to facilitate systemic acquired resistance in plants has been impaired by the observations of strong context dependency. In other word, the effect of microbe-induced resistance (MiR) against pest and pathogens is dependent of plant and microbe genetic make-up, as well as several abiotic components of the environment. Therefore, to better implement microbes in agriculture, we need to better understand induced-defences mechanisms and its dependencies.
The PhD project was part of the European research project “Microbe-induced Resistance to Agricultural pests” (MiRA), which aimed to increase knowledge with a view to better use MiR for crop protection. The MiRA project studied MiR mechanisms and impacts on plant performance and biocontrol organisms to improve our ability to predict the effectiveness of MiR according to the growing conditions. In this context, my PhD project aimed at evaluating the environmental dependency of microbe-induced plant resistance. To address this aim, I investigated the effects of abiotic factors as well as the tomato and microbe genotypes on resistance against insect pests and fungal disease. The study focused on the Solanum section Lycopersicon clade, mainly the species Solanum lycopersicum (tomato), and some of its wild ancestors belonging to different biogeographic origins. Concerning resistance-inducing microbes, some strains including arbuscular mycorrhizal fungi (AMF) and plant-growth promoting rhizobacteria (PGPR) were tested. The final aim of the whole project was to improve knowledge for a better efficiency and stability of plant-associated soil microbial products in order to promote a more ecologically-sound crop protection.
In the first chapter, I performed a greenhouse experiment for measuring the effect of different AMF inocula (Funneliformis mosseae, Rhizophagus irregularis, or both) on tomato plants (Solanum lycopersicum cv. ‘Moneymaker’) growth and defences against an insect herbivore under two conditions: a normal watering regime or drought conditions. I measured the functional, physiological and chemical traits of the plants. I found that AMF presence generally decreased plant growth, but increased chemical defences and resistance against generalist caterpillars. Such growth‐defence trade‐off was nonetheless dependent on the identity of the mycorrhizal inoculum and on soil water content. Under drought, inoculated tomato plants lowered their investment to defence and uninoculated plants lowered their growth.
In the second chapter, I tested the effect of different microbial inocula (AMF and PGPR) on the growth and defence of a domesticated tomato species, the standard commercial cultivar Solanum lycopersicum cv. ‘Moneymaker’, and three wild relative tomato species. I measured functional growth traits and insect herbivory as well as targeted and untargeted chemical traits of the plants. My results showed that domesticated and wild tomato are both affected by the microbial inoculation. I found that PGPR tend to increase, while AMF tend to decrease plant growth, similarly across species. Moreover, using targeted and untargeted metabolomics, I found that soil microbes deeply change the chemistry of the plants, both above- and belowground, in a species-specific manner. In this study, the response of the herbivore insect was more altered by the presence of AMF than the species of tomato.
In the third chapter, I experienced the effect of the PGPR Pseudomonas protegens on the growth, chemical defences, and pathogen resistance of a domesticated tomato species, the standard commercial cultivar Solanum lycopersicum cv. ‘Heinz’, hybrids of S. lycopersicum hybrid, and eight wild relatives tomato species. I measured functional growth traits and fungal symptoms as well as targeted and untargeted chemical traits of the plants. My results showed that both the domesticated and wild tomato species can change their phenotype when inoculated with P. protegens. We found that the PGPR tended to enhance fungal resistance, more so for the domesticated species. Moreover, we found clear effects of the PGPR applied on the root on leaf chemistry, but variable across tomato lines.
In the fourth chapter, I gathered a review article and a set of original research works done in collaboration with colleagues along the Microbe-induced Resistance to Agricultural pest (MiRA) European project. In the published review article, we proposed an approach that explicitly incorporates context-dependent factors into Induced-systemic resistance research in order to improve the predictability of ISR induction. We also discussed the need to raise awareness for mobilizing interdisciplinary efforts among researchers and stakeholders involved in the development of microbial inoculum. Then, I briefly presented collaborative studies that help to progress in elucidating the role of diverse biotic and abiotic factors in microbe-induced defences.
More than to inventory whether beneficial microbes help tomato plants to resist against pests, the project aimed to study how the surrounding environment and the identity of the biotic partners can influence the relationship between the plant and its belowground beneficial organisms, and how this affects its interactions with aboveground threat. My findings show which AMF strains may best perform under stressing drought conditions and that the use of a species-combined inoculum may improve efficiency in variable climatic conditions. All analyses demonstrate that both glycoalkaloid content and broader metabolome of the plant is modified by the either AMF or PGPR inoculum. Another upshot of the thesis is that certain PGPR may have a faster effect on plant growth than AMF and be less costly to plant development but also less efficient on insect pest control. One more outcome of the thesis is to show that domestication of tomato modified plant reaction to beneficial microbes but did not prevent modern cultivars to get profit from the symbiosis relationship. The results of this thesis bring new functional and metabolomic knowledge that can be used to fine-tune the use of beneficial microbes in agriculture and to serve as basis for further research
Generalized weights and other coding theoretic invariants
Get PDFAcceptée sur proposition du jury :
Prof. Elisa Gorla, Université de Neuchâtel, directrice de thèse
Prof. Jérémy Blanc, Université de Neuchâtel, membre interne
Dr. Lisa Seccia, Université de Neuchâtel, membre interne
Prof. Joachim Rosenthal, University of Zurich, expert externe
Prof. Hiram H. López Valdez, Virginia Tech, expert externe
Soutenue le 26 juin 2024Invariants play a crucial role in coding theory. They are in fact a valuable tool for classifying codes. Specifically, invariants help distinguish between non-equivalent codes. This distinction is relevant because equivalent codes exhibit the same decoding properties. However, determining whether two codes are equivalent is a hard problem.
In this thesis, we focus on a family of invariants called generalized weights. They were introduced in 1977 for linear block codes, but only became widely studied in 1991, when Wei proved that they measure the code robustness against wiretapping. The goal of this work is to define and study similar invariants for other classes of codes, such as codes over finite rings, sum-rank metric codes, and convolutional codes.
The first part of the thesis is dedicated to the notion of support for linear codes over finite commmutative rings. We investigate how to associate a combinatorial object, called latroid, with a code, and we explore which properties and invariants of the code can be recovered from it. We also show that the associated ideal is determined by the associated latroid.
The central chapters of the thesis concern sum-rank metric codes. First, we prove an anticode bound for this class of codes and we classify all the codes attaining this bound, i.e., the optimal anticodes. Then, we define the generalized weights for sum-rank metric codes in terms of optimal anticodes. We study their basic properties and we compute them in the case of maximum sum-rank distance codes.
In the final part of the thesis, we deal with convolutional codes. We give a definition of generalized weights that takes into account the module structure of this family of codes. After studying their basic properties, we prove that they can be computed by an algorithm that terminates in finite time. Then, we give upper and lower bounds for the generalized weights of maximum distance separable and maximum distance profile codes. We also discuss the notion of generalized column distances
Spatial analysis of transfer revenues streams (2014-2023)
No full textThis report analyses from a spatial perspective the origin of transfer revenues collected by clubs worldwide between 2014 and 2023 according to their parent association. In total, clubs earned no less than €75 billion: around two-thirds from international transfers and the rest from domestic ones. However, this proportion varies greatly from country to country
Crises, Migration and (Im)Mobility: Towards a Reflexive and Multilevel Approach
Get PDFScholarly inquiry into the intersections of migration, mobility, and crisis has mainly focused on international migration. The scope of this scholarship underscores the continuing influence of methodological nationalism in the field. We argue for a broader exploration of mobility (and immobility) perspectives. Accordingly, we embrace an encompassing understanding of crises as particular events and structural conditions with rather “extensive and large-scale changes and effects” (Bergman-Rosamond et al. 2022: 5). We further adopt what Bösch et al. (2020: 5) call a reflexive perspective “in which the constructivist dimension remains acknowledged” without relativizing a more objectivist view of “the real causes and effects” of the crises in question. Our approach builds on the concept of the Migration-Mobility Nexus (see Piccoli et al. 2024) and its interplays (continuum, enablement, opposition, and hierarchy) to study the crisis-induced shifts between migration, mobility, and immobility. To understand the complex and potentially intertwined ways in which crises interact with the Migration-Mobility Nexus, we propose to combine a multilevel analysis of experiences, practices and agency, perceptions and attitudes, and governance
Reconnaissance historique : la Suisse admet sa responsabilité dans un crime contre l’humanité sur son propre territoire
Get PDFLe Conseil fédéral a officiellement reconnu que la persécution des Yéniches et des Manouches / Sintés en Suisse constitue un crime contre l’humanité au regard du droit international actuel. Cette reconnaissance marque une avancée juridique majeure. Cet article explique le point de départ de l’avis de droit, en résume les principaux résultats et se prononce sur la réaction initiale du Conseil fédéral et de l’administration fédérale
Poster - Le mouvement Droit & Littérature
No full textPoster présenté lors du premier anniversaire de "Plume de Justice" (Université de Neuchâtel, 4 octobre 2024
TF 9C_263/2023 du 20 décembre 2023 - Paiement d’une indemnité pour le transfert de droits à bâtir sur une parcelle viticole appartenant à l’épouse et activité indépendante accessoire de l’époux
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Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants
No full textThe naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g. polyploidy, engorged nutritional rewards, and dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g. plant fragment degradation, ant-farmer communication, and antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: (i) free-living to ant-cultivated: loss of genes conferring stress response and detoxification; (ii) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis; and (iii) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by 3 leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes toward long-term ecological resilience of farming systems that have thrived across millennia