Orine, Dimitri

2024, Orine, Dimitri, Rasmann, Sergio

Plant-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.