The current global warming scenario predicts an increase of geographic expansion of pathogen distribution and epidemics. These future outbreaks represent a major threat to crops and are likely to cause significant yield losses. In this context, a major challenge is to identify the bases of resistance mechanisms allowing plants to cope with future epidemics and to develop, for instance new products for plant protection. Indeed, in the field, to grow and reproduce, plants have to face and simultaneously adapt to multiple stresses including abiotic (drought, salinity, temperature) and biotic (bacteria, fungi, viruses, insects). Often concomitant in natural conditions, these adverse abiotic and biotic constraints affect plant growth and ultimately productivity worldwide. While some genetic components of plant responses to environmental constraints were identified and characterized in the recent decades, our knowledge on the strategies developed by plants in response to combined stresses (biotic and abiotic) remain fragmented. More particularly, environmental changes such as a subtle but permanent increase in temperature (3-5°C), inhibits the major defense mechanisms against pathogen attack. Thus, the understanding and the identification of molecular components integrating environmental stimuli and controlling plant responses are of major interest for sustainable agriculture and global food security in the near future. This project will explore the contribution of calcium signaling modules in plants interacting simultaneously with biotic and abiotic factors. It is now well documented that most of the external stimuli induce a rapid increase in free calcium levels within plant cells and that these calcium variations are essential to coordinate the adaptive responses. To be informative, calcium increases need to be decoded and relayed by calcium-binding proteins also referred as calcium sensors to carry-out the appropriate responses. Although calcium signals are involved in most stress-signaling pathways, their direct manipulation in a targeted way (i.e. enhanced stress tolerance) would be tedious due to the diversity of actors participating in shaping these signals. One alternative would be to manipulate the function of the calcium-sensor proteins and/or of their targets involved in decoding the calcium signals. The originality of the project is to focus on the plant specific family of CalModulin-Like calcium sensor proteins (CMLs) due to their important role in both biotic and abiotic responses. The biological relevance of these calcium sensors, specific to plants, constitutes an emerging field in plant signaling research area and our goal is to demonstrate, using reverse genetic tools, that CMLs are central integrators of biotic and abiotic stresses responses. The project will be developed on two models plants: Arabidopsis thaliana and Tomato (Solanum lycopersicum) and will mainly consider the impact of temperature increases on the interaction of both Arabidopsis and Tomato with two of the most destructive plant pathogenic bacteria worldwide, Ralstonia solanacearum (Rs) and Pseudomonas syringae pv. Tomato (Pst). Tomato was selected because it is not only a widely cultivated species highly sensitive to Rs but also an excellent model in plant-pathogens interaction studies. The functional characterization of some selected CMLs, associated to environmental stresses, will be performed in response to Rs and Pst infections in conditions of a weak and permanent increase of temperature (3 to 5°C) and a particular attention will be dedicated to the molecular processes controlled by these CMLs through the identification of their downstream targets.

Expansion of some harmful root parasitic weeds (Striga, orobanche, and Phelipanche species) in numerous economically important crops is becoming more than worrying and is a serious threat to food security in some area of Africa. If we consider the broomrape species Orobanche cumana, it causes important losses to the production of sunflower seed in countries surrounding the Black Sea, in Southern Europe and now in growing area of France. Unfortunately, no sustainable or efficient methods to control these various root parasitic weeds are presently available. O. cumana is a holoparasite devoid of chlorophyll which is unable to carry out photosynthesis and totally relies on its host for its water, mineral, and carbohydrate supplies. Like for other species of Orobanchaceae, two key steps must be completed by this weed for establishing parasitic interaction. It must perceive specific molecular signals produced by host roots in order for its seeds to germinate, and it must develop a novel specific organ, the haustorium, to invade host root tissues and connect to host vascular system. The molecular processes underlying these two steps are largely unknown. Progress has been hampered by the lack of genomic resources in orobanche and the lack of protocols allowing reverse genetics. The objectives of the proposed project are i) to develop new molecular tools to investigate the two main steps of parasitic development and ii) to develop an innovative and sustainable biocontrol technology for management of these Orobanchaceae pests. One partner of the project has discovered a new class of regulatory peptides, the miPEPs, which will play a pivotal role in the project. These peptides are encoded by primary transcripts of miRNAs. Each miPEP stimulates the transcription of its own encoding transcript, leading to the production of higher amount of the corresponding miRNA and consequently to a downregulation of specific target genes. This natural molecular regulation of gene expression can be obtained with synthetic miPEPs, so that specific stages of plant development can be perturbed temporally by exogenous treatment with appropriate miPEPs. The project will consist in two main Tasks: Task 1: to identify O. cumana miPEPs potentially involved in the regulation of seed germination/haustorium formation of O. cumana (based on RNAseq data already available and RACE-PCR analyses), to identify sunflower miPEPs most likely involved in regulating sunflower immunity (based on RNAseq data), to produce the corresponding synthetic candidate peptides and to assess the activity of O. cumana synthetic miPEPs on seed germination and haustorium differentiation (using specific and original in vitro assays). Task 2: to select the synthetic O. cumana and sunflower miPEP candidates and evaluate their capacity to negatively affect parasitism by either decreasing broomrape growth and infection or improving sunflower resistance (using in vivo pot culture assays), and in the light of the obtained results to define the miPEPs capable of controlling two other parasitic plant – plant interactions: Phelipanche ramosa – oilseed rape and Striga hermonthica – maize. The expected result of Task 1 is to increase our knowledge on key molecular mechanisms underlying a complex parasitic interaction by discovering important genes of O. cumana and sunflower which are involved in broomrape parasitism. The expected results of Task 2, to be exploited by a startup company, will be to provide a new phytosanitary method to control broomrape (and possibly witchweed) parasitism with highly specific and biodegradable natural substances.

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.

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.