Orobanche cumana is an obligate root parasitic plant that infects sunflowers, leading to significant yield losses. Broomrape seeds in the soil germinate only by perceiving molecules produced in the sunflower root exudates. Using the genetic resources of Helianthus, we have identified accessions that induce the germination while others do not. Genetic and genomic approaches will identify candidate genes involved in the biosynthesis of the stimulating molecules. An approach without a priori will also be carried out by fractionation of sunflower root exudates and by analyzing their germination capacity and their molecular composition. We will identify the receptors of the molecules in broomrape using functional biochemical approaches and by analyzing their diversity. In addition to fundamental knowledges, our results will lead to the production of new resistant sunflower varieties and new control methods.

Plants have evolved an innate immunity that relies on the recognition of pathogenic determinants. A major consequence of recognition is a rapid and massive transcriptional reprogramming of defense genes that involves changes in chromatin composition and remodeling. Nevertheless, we are far from understanding the chromatin remodeling events that are associated either with the development of disease or with the activation of plant immunity. Moreover, from a pathogen’s perspective, epigenome reprogramming by bacterial pathogens represents a potent virulence strategy to take the control of host gene expression, although the underlying mechanisms remain poorly characterized. Another unexplored question is how chromatin changes occurring at a distance from the infection site may contribute to biotic stress memory. This highly innovative and ambitious project is aimed at investigating for the first time and in a cell-specific manner the chromatin remodeling events that are associated either with the development of plant disease or the activation of plant immunity in response to a bacterial bioagressor. Bacterial wilt caused by Ralstonia solancearum is one of the most destructive bacterial plant diseases because of its extreme aggressiveness, worldwide geographic distribution and broad host range (more than 200 plant species including Solanacea, among which tomato). The Ralstonia PopP2 acetyltransferase effector was previously shown to targets several WKRY defensive transcription factors (TFs) to block their trans-regulating functions needed for defense gene expression, inhibiting basal resistance. PopP2 also targets various epigenetic readers and dissociates them from chromatin. Therefore, it does represent a powerful tool to study effector interference on host epigenome. By using cutting edge technologies and experimental approaches (GFP strand, INTACT, RNA-seq, ChIP-seq, Hi-ChIP), we will try to answer the following questions : (1) How does PopP2 effector affect the host epigenome? For this, we will investigate how the transcriptome responses can be linked with chromatin dynamics impacted by PopP2 that inhibits basal resistance or activate strong immune responses in susceptible and resistant Arabidopsis plants, respectively. (2) What are the chromatin changes induced by Ralstonia solanacearum in infected cells of Arabidopsis and tomato? This analysis will be performed in purified infected cells to provide the necessary resolution. In addition, we would like to investigate how meristematic cells respond to the infection by Ralstonia and whether particular chromatin features shape the plant resistance response to subsequent pathogen attacks (priming). (3) Can disease resistance be improved by manipulating epigenetic processes? To assess the role of particular chromatin modifications in Arabidopsis and tomato response to Rs, we will use reverse genetics (T-DNA insertions, VIGS or CRISPR genome editing) and overexpression approaches. Overall, this project is expected to provide key insights into microbial pathogenesis and reveal important regulatory epigenetic mechanisms of plant immunity. The obtained knowledge will be exploited to determine how epigenetic-related mechanisms can be manipulated to modulate plant response to microbial infection. The long-term goal of this research proposal is to improve current disease management strategies.

Albeit by no means new, collaboration in science has recently gained unprecedented momentum and visibility. Commonly presented as “a good thing”, it has become an imperative. This holds especially true for sustainability science, a recent and expanding problem-driven science that focuses on the dynamic interactions between nature and society and aims to create and apply knowledge in support of decision making for sustainable development. Researchers in this field are strongly encouraged to work with colleagues from other disciplines and actors from outside academia. Yet, little is currently known about how collaborations transform the work practices and identities of researchers and contribute to the shift towards more sustainability. COLLAB² will offer both a broad and in-depth view of inter- and transdisciplinary collaborations in sustainability science. It will pursue the four following goals: 1) elaborate a typology of these collaborations, based on a thorough investigation of their characteristics; 2) describe and analyse their dynamics: how they unfold over time, what stimulates or on the contrary hinders them, at various levels; 3) explore their effects on the practices, roles, identities and trajectories of researchers and their collaborators, and their capacity to contribute to the shift towards more sustainability. A fourth cross-cutting goal is to conduct this research and disseminate its results in close association with sustainability scientists and their partners, so that this project about collaboration will itself be highly collaborative (hence the acronym COLLAB²). COLLAB² will explore the full scope of collaborations in sustainability science in three institutional settings aiming to foster them: CNRS’s Zones Ateliers and Observatoires Hommes-Milieux, and biosphere reserves. It will produce a balanced and multi-level analysis of collaborations, and address their different dimensions (material, cognitive, relational and affective) in the long run. A common research framework will be adopted to allow a cross analysis of the data. It will rely on a mixed method, combining bibliometric tools, a national questionnaire that will be disseminated simultaneously in the three institutions, and an ethnographic survey of a sample of diversified collaborative projects. COLLAB² will devote paramount attention to the perspectives of participants in collaborations, which is crucial given the importance of their human factors but has seldom been addressed so far. COLLAB² will bring together six social and life scientists with strong personal experience of collaborations in sustainability science and wanting to explore them together and with other partners. A dyad of collaborators from each institution investigated will be closely associated to the work of the consortium throughout the project. This will enable us to experiment with a process of participative and iterative reflection through the sharing of experiences and ideas beyond the consortium, leading to new knowledge and mutual learning. COLLAB² will thus make an invaluable contribution to the emerging scientific field of collaboration studies. Its results will be disseminated to a large and diversified audience, using well-adapted language and through a wide array of communication channels (articles in academic and technical journals; conferences and seminars; presentations to the institutions investigated; short videos; interactive website). It will help sustainability scientists and their collaborators to identify the factors and effects of collaborations, overcome their inherent difficulties and form a community of practice. It will provide science policymakers and relevant ministries with concrete recommendations to improve collaborations in sustainability science and craft sound research policies in the Anthropocene.

Plants belonging to the legume family are able to interact with nitrogen-fixing soil bacteria collectively named rhizobia. This symbiotic interaction referred to as the legume-rhizobium symbiuos (RLS) leads to the formation of a facultative organ called the root nodule, inside which atmospheric nitrogen is fixed by the bacteria to the benefit of the plant. In the soil, legumes also face threats from root-knot nematodes (RKN) that induce the formation of a new root organ called a gall containing hypermetabolic, multinucleate and giant feeding cells that serve as unique source of nutrients. These seemingly very different interactions nevertheless share some common genetic pathways. Nodule development is specifically controlled by the CCAAT box-binding transcription factor NF-YA1. Interestingly, we have recently shown that NF-YA1 is also strongly upregulated in RKN-induced galls and that nf-ya1 mutants are affected in both interactions. NF-Ys are considered pioneer transcription factors modulating local chromatin accessibility and hence developmental switches. In addition, we showed that NF-YA1 regulates the expression of many genes in response to rhizobia, including emerging actors of chromatin-based gene regulatory mechanisms, the long non-coding RNAs (lncRNAs). The objective of the MELONOD project is to decipher the common and specific mechanisms by which the NF-YA1 pioneer transcription factor regulates both the beneficial rhizobial symbiosis and the pathogenic interactions with RKN in the model legume Medicago truncatula. MELONOD will be subdivided in three axes: (i) MELONOD will deliver a list of direct NF-YA1 target genes during RLS and RKN infection, as well as a list of common target genes during both interactions. This will be achieved by a combination of RNA-seq and ChIP-seq approaches ; (ii) MELONOD will characterize the chromatin landscape at NF-YA1 target sites through four complementary approaches. Nucleosome occupancy especially at promoters of direct targets defined in (i) will be investigated using ATAC-seq. Whole-genome bisulfite-sequencing will be performed to identify differentially methylated regions in the promoters of NF-YA1 targets in nodules and galls. We will perform comparative ChIP-seq analyses in WT and nf-ya1-1 mutant to investigate if NF-YA1 binding during RLS and RKN infection influences repressive or permissive histone modifications at target gene promoters. To probe for the presence of NF-YA1-dependent chromatin loops, we will use Hi-C on WT or nf-ya1-1 mutant nodules and galls; (iii) LncRNAs have known roles in chromatin-based gene regulatory mechanisms and are thus promising candidates to explain the pioneer role of NF-YA1 during both interactions. We will characterize four NF-YA1-regulated lncRNAs including NANO1, which is strongly upregulated at the onset of both interactions. We will generate M. truncatula knock-down (KD) and knockout (KO) lines using RNA interference, CRISPR-Cas9, and Tnt1 transposon insertion lines. Overexpression constructs will also be tested. To investigate the underlying mode of action of these selected lncRNAs, target chromatin regions will be identified genome-wide by Chromatin isolation by RNA purification and proteins bound by these lncRNAs will be identified using RNA immunoprecipitation followed by mass-spectrometry. Finally, the potential regulatory role of these lncRNAs on chromatin loop formation and target gene expression will be investigated using Hi-C in transgenic lines with modified lncRNAs levels. These approaches should allow a better understanding within the same host plant of a fascinating case of convergence between two plant development programs, one in mutualistic and the other in parasitic interactions. This knowledge will allow further development of applied innovative strategies for increasing nematode resistance without altering symbioses, or even promoting symbiosis in legume crops.

Nitrogen is limiting for plant growth, which explains the massive use of nitrogen fertilizers in agriculture. However, nitrogen fertilizers present a number of drawbacks, including a large waste of fossil energy for their production and use, and a strong pollution of water resources (nitrates) and atmosphere (greenhouse gas). The development of sustainable agriculture practices more respectful of our environment therefore needs to find alternatives to nitrogen fertilizers. In contrast to other plants, legumes can grow without addition of exogenous nitrogen. Indeed, these plants are able develop a symbiotic relationship with soil bacteria called rhizobia, which possess the capacity to reduce atmospheric nitrogen into ammonium to the benefit of their host plants. Thanks to this unique property, legume plants can increase nitrogen content in the soil, which can be beneficial to other crops, like cereals, cultivated either in association or in alternance (rotation). In addition, legumes are also cultivated for their own properties and are the basis of human food and animal feed worldwide. Biological nitrogen fixation by rhizobia takes place in specific root organs, called nodules. Like all plant organs, root nodules have a limited life-span, and eventually enter a senescence process characterized by the coordinated death of both bacteria and plant cells. This senescence process either results from nodule aging (developmental nodule senenescence) or can be triggered prematurely by adverse environmental conditions. In all cases, nodule senescence results in a decline of nitrogen fixation, characterized by a color change from pink to green (due to degradation of the plant leghemoglobin, a hallmark of active nitrogen fixation). Preventing or delaying nodule senescence (i.e. allowing nodules to stay pink) is therefore a promising strategy to prolong nitrogen fixation and thereby increase legume crop yields. However, although an impressive knowledge on the early stages of endosymbiosis has been gained in the past decades, the latest stages, notably nodule senescence, remain poorly understood. The main objective of this proposal is to describe the mechanisms acting in symbiotic nodules, both in plant and bacterial cells, to regulate the transition between an active nitrogen fixation and the onset of senescence (whether developmental or environmentally-induced). The project will use an integrative approach carried out in parallel in the two symbionts. This objective will be achieved thanks to the specific structuration of the proposed consortium, involving a tight collaboration between plant biologists and microbiologists. In a first part of the project, a without a priori approach based on a combination of transcriptomics and genetics will allow the identification of key legume and rhizobial genes linked to nodule senescence, either developmental or environmentally induced. In a second part of the project, several biological actors/pathways already known or predicted to be involved in nodule senescence will be characterized in details: phytohormonal pathways, cysteine proteinases, nitric oxide and bacterial toxin/antitoxin systems. Connections between these actors/pathways, or with genes identified during the first part of the project, will also be looked for. Most of the studies will be conducted on the model symbiosis between Medicago truncatula and Sinorhizobium meliloti, but the ultimate goal is to provide targets to delay nodule senescence of agriculturally relevant legumes. Thus some of the strategies already known to delay nodule senescence in the model symbiosis will be transferred in a legume crop, pea, and its symbiotic partner, Rhizobium leguminosarum.