Pesticides are of limited use against bacterial diseases in crops due to a lack of effective and non-toxic molecules. Thus, genetic selection of resistant crops remains the most effective approach to control bacterial pathogens. Resistance breeding requires a conceptual jump to efficiently design significant and durable resistance to a large variety of pathogens in a large number of crops simultaneously. The CROpTAL project aims at identifying plant susceptibility hubs in major crops (cereals, citrus, legumes and brassicaceae) targeted by Xanthomonas virulence-promoting TAL (Transcription Activator-Like) type III effectors. These conserved susceptibility targets could then be used for marker-assisted breeding of loss-of-susceptibility by selection of inactive variants of those hubs. These results will contribute to the development of durable resistance to a broad range of bacterial pathogens in the selected crops.

In the context of climate change, it appears essential to unravel the mechanisms governing abiotic stress tolerance in higher plants, in order to build predictive models and use this knowledge to assist selection and design of stress tolerant crops. We have previously uncovered remarkable adaptations in seed mitochondria, which because of the ability of seeds to survive desiccation, display impressive tolerance to abiotic stress. In particular, seed mitochondria accumulate high levels of small heat shock proteins (sHSP) and late embryogenesis abundant proteins (LEA). The sHSP are the most widespread but less conserved HSP. They contribute to the molecular chaperone network that assists protein biogenesis and homeostasis under stress conditions (sHSPs are stress inducible). In eukaryotes, mitochondrial sHSP (M-sHSP) have only been identified in plants and insects. LEA proteins are highly hydrophilic proteins, generally intrinsically disordered, which accumulate in desiccation tolerant organisms, and whose functions still remain largely enigmatic. The MITOZEN project aims at deciphering the molecular function and physiological role of the mitochondrial sHSP and LEA proteins (M-sHSP and M-LEA) in the model plant Arabidopsis thaliana. The genome of Arabidopsis harbors 17 sHSP genes (including 3 M-sHSP) and more that 50 LEA genes, among which we have recently identified 5 M-LEA genes. The molecular functions of the M-sHSP and M-LEA will be explored using biochemical and biophysical approaches to study recombinant proteins produced in Escherichia coli. Their structural features and protective activities (oligomerisation, secondary structure, chaperone activities, membrane protection) will be examined in the context of temperature stress and dehydration using a large panel of techniques and in vitro assays. The goal is to determine the potential molecular functions of the different M-sHSP and M-LEA in the context of stress tolerance (desiccation in seeds, high temperature in seeds and plants). A reverse genetics approach will be developed in Arabidopsis to explore the role of M-M-sHSPs and M-LEAs in the physiology and development of plants. Single and multiple knock-out mutant lines will be constructed, as well as overexpressors using an inducible system. Their phenotypic characterization will focus on seed development and abiotic stress tolerance of plants, including mitochondrial function. The integration of data provided by these multidisciplinary approaches (bioinformatics, biochemistry and biophysics, genetics, physiology) will shed light on the function and importance of the different M-sHSP and M-LEA in the development and stress tolerance of plants. It will also increase knowledge about molecular chaperones and in particular with respect to their yet unexplored role in the context of dehydration, and will shed novel light on the function of LEA proteins.

Plant responses to biotic aggressions involve a great diversity of molecules including regulatory proteins and hormones. Among these actors, small secreted peptides, also named peptide phytohormones or phytocytokines, may directly interact with pathogens or act in signalling and cell-to-cell communication. They are produced from non-functional precursors through a maturation process, making characterization difficult only on the basis of their gene sequences. Only a small fraction of the genes liable to encode these secreted peptides has been described and their impact and diversity appears to be seriously underestimated. The main goal of STRESS-PEPT is to better understand the plant responses to biotic stress at the peptidome level and to characterize new molecular actors involved in defence mechanisms. Based on our experience and previous results, we plan to develop and apply a multidisciplinary genome-wide approach combining bioinformatics, differential transcriptomics and peptidomics to identify new secreted peptides in Arabidopsis and to describe their contribution to plant responses to different representative biotrophic and necrotrophic pathogens (oomycete, fungus and bacterial elicitor). The proposed methodology is organized in three complementary tasks: (i) An original bioinformatics pipeline will be used to screen the Arabidopsis thaliana genome in order to identify genes encoding precursors of secreted peptides, to cluster and classify them in gene families by homology and phylogenetic profiling and to predict the putative mature peptides through a sensitive conserved motif searching method ; these predictions will be integrated to RNAseq transcriptomics analyses applied on Arabidopsis in presence or absence of the different pathogens in order to tag the fraction of the secreted peptide precursor genes that are transcriptionally regulated by pathogen aggression(s). (ii) The same biological samples will be used to prepare extracts of peptides, from apoplastic fluids and total extracts, through an original protocol optimized for efficient mass spectrometry (MS) analysis: a LC-MS/MS based peptidomics approach will be applied on the different peptide extracts for the identification and the differential quantification of the secreted peptides and to characterize their post-translational modifications. (iii) A selection of promising peptides, based on transcriptomics and peptidomics data, will be made for functional analyses including assays on knock-out mutants and overexpressing transgenic lines. Synthetic peptide treatments will be performed in order to understand and validate their role in plant-pathogen interactions. The STRESS-PEPT consortium gathers bioinformaticians, molecular biologists, biochemists and plant pathologists expert of each studied pathosystem as well as a proteomics platform. The already established collaborations between these partners will ensure close cooperation and synergy throughout the 4 year project, and ensure obtaining results of high interest for the plant biology community. All the data generated will be stored and organized for efficient querying in a relational database publicly available at the end of the project. STRESS-PEPT will lead to significant advances in the discovery of new secreted peptides which are key players in danger sensing and the modulation of immune responses. According to their conservation among plant species, these peptides might be used in innovative strategies aiming at jointly optimizing plant quality and resistance, and should open new opportunities for sustainable crop management.

The urbanization of society has gradually separated humans from the plant world. Most people have forgotten the names of plants and their potential uses. Yet there is a growing awareness that biodiversity is a treasure we must preserve and transmit to future generations. The identification of plant species is a necessary step to understand our environment. However, for most people, botany remains difficult to understand and to learn. It is not easy to decrypt botanical literature because it requires a solid theoretical background. In the ReVeRIES project (French acronym that means “dreams” and that stands for Interactive, Fun and Educational Plant Recognition on Smartphones), we propose to use mobile technologies in order to help humans recognize plants that surround them. We believe that a promising way to recreate the relationship between modern human beings and their natural environment is to provide smartphone applications that help them recognize and learn about plants. The ReVeRIES project relies on a mobile application called Folia and developed during the ANR ReVeS project. This application is capable of recognizing species of trees and shrubs (taller than 1m20 and originating from France) by analyzing photos of their leaves. This prototype simulates the behavior of a botanist when trying to determine the plant species, which makes it different from all the other tools available on the market. In the context of ReVeRIES, we propose to go much further by developing the following aspects: game-based mobile learning, multimodal images recognition and citizen sciences. First of all, we intend to design mobile learning games that will help users learn about plant characteristics and especially learn the methods, used by expert botanists, to recognize plant families, genera and species. In order to motivate children and botanical neophytes to learn about plants and explore their natural environment, we also intend to use game mechanics for creating fun activities based on plant recognition. The users will be able to improve their skills by comparing their results to those found by the recognition algorithm. Concerning the image recognition process, we intend to extend the previous prototype to the main exotic woody trees and shrubs. Moreover, we aim to take into account various organs of the plant. This multimodality is essential if we want users to learn and practice the correct recognition method, for which botanists use a variety of organs (i.e. leaf, bark, size of plant, flower, fruit, etc.). In addition, the use of organs should greatly improve the algorithm’s accuracy. In terms of image processing, the work done on the leaves cannot be extended directly to flowers, fruits and barks. This will greatly increase the complexity of the data fusion process. Finally, we intend to explore ways in order to enhance social awareness of our natural resources and to support citizen science. The geolocated photos and information taken with the application and validated by experts, could be transferred to specialized networks, such as Tela Botanica, integrated into the OpenStreetMap geographic information system and mobilized by local institutions to support actions and projects involving citizens. This addresses problems related to the field of Volunteered Geographical Information. The project raises many scientific challenges in TEL (Technology Enhanced Learning), Serious Game, image analysis, data fusion, HCI, and also in the field of collaborative environmental inventories. The possible impacts are numerous: teaching of botany at different levels and with various learning audiences, collective intelligence, citizen sciences, nature preservation and environmental collaborative games. In addition to citizens interested in nature, this system could be very useful for teachers and their students, botanists and also nature parks.

Natural grasslands and cereal fields play fundamental role in supporting biodiversity conservation and sustainable food production. Natural grasslands (including grasslands within a protected area and unprotected grasslands) and cereal fields provide multiple ecosystem services, but also involve significant trade-offs (e.g., food production vs. soil carbon sequestration). Yet, unlike aboveground plants and animals, the capacity of European protected areas to conserve plant and soil microbial diversity and ecosystem services in natural grasslands under global environmental changes is virtually unknown. Moreover, we know very little about how cereal fields will respond to multiple co-occurring global change stressors, such as drought, pesticides and over-fertilization, which are threatening the conservation of soil biodiversity and function as well as food production. Objectives 1 & 2 will evaluate whether protected areas promote soil biodiversity and multiple ecosystem services in European natural grasslands, and will monitor the microbial diversity and function in cereal fields. To such an end, we will conduct a European-level survey across grasslands’ triplets with different land use intensities (from protected and unprotected natural grasslands to maize and wheat fields). The sampling in cereal fields will support the monitoring that the Crop Microbiome Initiative started in these sites 3-5 years ago. In Objectives 3 & 4, GRASS4FUN will further investigate whether multiple global change stressors impact the microbiome and function of European natural grasslands and cereal fields. To do so, we will use combine the modelling and mapping of soil biodiversity and function across climate and land cover change scenarios with a manipulative study using microcosms subjected to multiple global change stressors. GRASS4FUN will be performed in close collaboration with a stakeholder advisory board to facilitate engagement and uptake by end-users, policy makers and society with the fundamental goal of providing ground-breaking knowledge to increase the resilience of grasslands to global stresses and protect European biodiversity, including organisms living in soils. GRASS4FUN will provide critical knowledge for the long-term economic benefits of the EU, and it is in line with multiple European-level programs such as Farm to Fork Strategy, EJP Soil and European Green Deal.