INRAE

The microbial community in the human intestine is crucial to the health and nutrition of the host. Loss of the fragile balance within this complex ecosystem is involved in numerous pathologies, including inflammatory bowel disease (IBD). The incidence of IBD is increasing and affects individuals in challenging years of their lives, with immunosuppressive treatments that are not always effective. IBD results from a combination of genetic predisposition, alteration of the gut microbiota, and environmental influences. Thus, deciphering the host-bacteria crosstalk will improve our understanding of IBD and enable new preventive and therapeutic strategies. Caspase recruitment domain 9 (Card9), one of the IBD susceptibility genes, codes for a protein involved in the response to fungi and bacteria. Sokol and colleagues showed that Card9-/- mice have an increased susceptibility to colitis, due to an altered gut microbiota that is not able to metabolise tryptophan into aryl hydrocarbon receptor (AhR) ligands. In humans, comparable mechanisms seem to be involved, as microbiota of IBD patients exhibit impaired production of AhR ligands, which mirrors the Card9-/- genotype. We aim to decipher the mechanisms involved in the modulation of the microbiota and its metabolic activity by Card9. For this purpose, we will take advantage of a strong collaborative environment and cutting-edge techniques, including gnotobiotic animals, cre-lox technology, transcriptomics, metabolomics and systems biology. Specifically, we plan to identify (i) new pathways and cell types involved in the modulation of the microbiota and its metabolic activity, and (ii) microorganisms and metabolites activating AhR receptors in the gut. This highly innovative and integrative project will allow me to expand my conceptual and technical knowledge of the gut-microbiota interface, acquire new key skills and strengthen my scientific network.

Biological nitrogen fixation (BNF) is one of the key agroecosystem services provided by legumes. Legume crops have a positive impact on the atmosphere and soil quality: i) by lowering emissions of greenhouse gases compared with other crops grown under mineral fertilisation and ii) by supporting BNF to the following crop when grown as components of crop rotations. This results in cost savings on synthetic fertilisers and fossil energy inputs in the system and on tillage, due to improved soil structure. However, factors such as insect attack, foliar disease and root microbial infection have a direct or indirect influence in reducing nitrogen fixation capacity and yield. Therefore, control of root-feeding organisms is essential for maximisation of nitrogen uptake by legumes. Conventionally, agrochemicals have been used to protect legume crops from pest and diseases, but their indiscriminate use has resulted in pest resistance and secondary pest resurgence, and they are detrimental to beneficial organisms for crop defence. The importance of driving reforms in response to the European commitment to sustainable agriculture and food production is directing my research interests towards a long-term mission that enables implementation of a new agricultural concept regarding food production that is safer for humans and the environment. The proposed project will use peas as a plant model to look for innovative strategies for reducing the dependence on chemical inputs, applying cutting edge technologies to leverage the use of beneficial soil microbes in the crop system. I suggest a pest management strategy to control nodule feeder insects by means of entompathogenic fungi (EPF). By exploring tritrophic interactions in plant-microbe-insect relations, this action seeks to evaluate whether EFP inoculated into legume crops can invade plant and nodule tissues, protect plants from pathogens and insects, influence BNF and affect the behavioural responses of aboveground insects.

In bacteria, the rigid external cell wall (CW) and the intracellular actin-like (MreB) cytoskeleton are major determinants of cell shape. Synthesis and chemical composition of the CW, a three dimensional polymer network that is one of the most prominent targets for antibiotics, are well understood. However, despite decades of study, little is known about the complex CW ultrastructure and the molecular mechanisms that control cell shape in time and space. MreB homologues assemble into dynamic membrane-associated structures thought to control shape by serving as organizers for the movement and assembly of macromolecular machineries responsible for CW biogenesis. However, the mechanistic details used by the MreB cytoskeleton to fulfill this role remain to be elucidated. We will combine powerful genetic tools available in the model Gram-positive bacterium Bacillus subtilis with modern high-resolution fluorescence microscopy techniques and atomic force microscopy (AFM) to study the role of the MreB cytoskeleton and CW synthesis proteins in cell shape determination and maintenance. Additionally, the role of mechanical forces in the control of CW organization will be evaluated.

Rising atmospheric CO2 concentration, increasing temperature and altered precipitation patterns dramatically impact the terrestrial biosphere with important consequences for all biogeochemical cycles. Predictions of carbon (C) and water exchange between vegetation and the atmosphere require detailed mechanistic understanding of how plants control water loss and C gain through their stomatal pores. Currently, global circulation models incorporate formulations of stomatal conductance (gs) based on stomatal optimisation theory. However, these models ignore gs regulation: (1) during night time, despite clear evidence for significant nocturnal transpiration, (2) in non-vascular plants and (3) during leaf development and senescence. To reduce the uncertainty associated with current C and water fluxes in models, we need to incorporate robust predictions of gs in response to novel environmental conditions (higher temperature, decreased water availability and elevated CO2). To fill these gaps, USIFlux, will develop a novel tracing technique to measure gs during the dark, when fluxes are an order of magnitude smaller than during the day. To do so, we will combine measurements of COS (carbonyl sulphide) uptake with CO18O fluxes and changes in the oxygen isotope composition (δ18O) of water in leaves. We will relate the response of gs at night to changes in gs during the day and in response to drought and elevated CO2. These measurements will be coupled to an experiment to investigate stomatal regulation during leaf ontogeny and in different life forms. Here, we will challenge the stomatal optimisation theory in life forms lacking active stomatal control (mosses and brackens) and during leaf development, when leaf construction costs constrain the optimisation of C gain. Empirical formulations arising from these experiments will be incorporated into large-scale soil-vegetation-atmosphere transfer models to explore their impact at larger scales.