Summary Tropical tree plantations provide indispensable renewable goods to the global market and family farms represent the majority of their surface area and production. To ensure the sustainability of plantation systems, environmental and socio-economic conditions should remain favorable during several decades. How can such conditions be ensured when the environment is changing? Even if the local consequences of global increase in temperature are difficult to assess, the farmers will probably face a more variable climate, with probable changes in rain patterns. Moreover, all natural resources have recently faced hugely variable prices related to variations in global demand. High prices attract new investors and drive the extension of plantations into new areas, inducing land-use changes and changes in farming structures. The final aim of the project is to analyze how smallholder’s tree plantations can adapt and keep sustainable whereas they face variable climatic conditions and deep changes in their socio-economic context. Do farmers perceive these risks and do they initiate adaptive strategies? Rubber tree-based systems in Thailand will be used as a model of tropical family plantations integrated in a major global commodity channel. The project will assess both the specificities of rubber cropping and the more general features of tree plantations. The originality of the project relies on the multi-disciplinary approach of both the characterization of changes and their consequences on rubber plantations and the related risks for farmers. Plant and soil sciences will be associated to social sciences and economics. We will analyze the way socio-economic factors interact with biophysical factors to determine farmers’ vulnerability or adaptability to changes. This will require the identification of relevant indicators to measure farmers’ adaptation, and the impacts of changes on sustainability and resilience of the systems. We will refer to the Sustainable Livelihood Framework (Ellis, 2000) to represent the household/holding , combined with the OECD risk matrix (2009) to assess households’ viability. We will focus on two major factors, (i) the type of holdings, particularly the emergence of new investors and (ii) the share-cropping contracts that frame the management of plantations. The main biophysical risk relate to climate changes and to the extension of plantations in new and more adverse areas. We will evaluate the risks at plot or farm levels, as well as potential externalities, in terms of soil sustainability (soil fertility preservation related to soil physical quality and soil functional diversity) and tree adaptation to water stress. Specific ecological constraints linked to the different cultivation area will be considered. In the North-eastern rubber extension area, the climate is drier and the soil fertility is low, whereas in the traditional area (South) continuous rubber cropping occurs for more than 50 years (third cycle). In the North, the specific issue of rubber installation in mountainous area will particularly focus on the effects of terracing, considering the impact on water flow and water balance. A typology of rubber farming systems and of practices will be proposed from socio-economic survey, particularly regarding land management and latex harvesting systems. The impact of practices on economic performances, soil physical and bio-functioning will be evaluated through specific indicators that will be developed or adapted in the perspective of multi-criteria evaluation of plantation systems. The information will be integrated at different scales from plot to farm and watershed and shared with stakeholder through a co-innovation platform. Beside the specific case of rubber plantations, a more generic output of the project is to determine, through modelling and risk framework analysis, the most significant indicators to be observed to assess the long-term adaptation and sustainability of tree-based family farms.

Phosphorus (P) is a fundamental element for plants. The depletion of the mineral P reserves as a chemical fertilizer will occur suddenly due to the growing world demand for agriculture. In addition, the excessive use of mineral fertilizers causes major dysfunctions of the agrosystem in the medium and long terms. This requires us to quickly discover sustainable alternatives. Large quantities of organic P and inorganic P, adsorbed to soil constituents, represent important reservoirs of P. Exploitation of these P sources, which are not readily available for crops, could be a promising avenue in agriculture. Nematodes are the most abundant animals on Earth. They are ubiquitous and play essential roles in regulating nutrient cycles in ecosystems. Within the rhizosphere, nematodes can greatly improve plant P availability from these poorly-available P sources. However, taking nematodes into account as biological beneficial actors for the increase in plant P availability has so far been largely neglected. Therefore, the mechanisms by which nematodes affect soil P fluxes and the controlling factors, both abiotic and biotic, are unknown. The O-NEMATO-P (Optimizing NEMATOde-driven P availability) project aims to explore the roles of soil nematodes in improving the availability of P for crops from poorly-available sources. The project focuses on ecological processes, mechanisms and controlling factors. We plan to explore and use nematode functional traits to relate the structure of soil nematode communities to P fluxes at the soil-plant interface, without neglecting the usual metrics of community diversity. In order to feed into the agronomic work carried out in agroecology, we are working to develop a "Pho-nem" indicator which will provide information on the capacity of an agricultural practice to intensify the ecological processes involved in the mobilization of P from sources that are not readily available for crops. To achieve this goal, advanced innovative techniques (18O labeling technique, the phytate model, multi-species co-inoculation, and bacterial strains transformed by GFP) will be used in conjunction with modeling and classification techniques by machine learning. The knowledge acquired will provide important fundamental information on the role of soil nematodes on plant P availability from poorly-available P sources. In the current framework of agronomic innovation fueled by agroecology and the ecological intensification of soil functions, our results can be used to design and evaluate the sustainability of agricultural practices by encouraging the exploitation of P sources and thus limiting the use of expensive mineral fertilizers that impact the environment.

MYCOTRANS aims at producing basic knowledge on the functioning of symbiotic exchange between plant roots and fungal symbiont, a beneficial interaction crucial for plant nutrition. MYCOTRANS will focus on the symbiotic ectomycorrhizal (ECM) model association Pinus pinaster – Hebeloma cylindrosporum, because this fungal species is the only one easily transformable with Agrobacterium, enabling genetics studies to be performed. Several transcriptional studies have revealed mycorrhiza-induced fungal membrane transport systems involved in K, N and P nutrition, but surprisingly, a member of the CDF (Cation Diffusion Facilitator) family was identified as the most mycorrhiza-induced transporter. So far, we have studied transport of macronutrients as potassium and phosphate, but we hypothesize that this micronutrient transporter, as other significantly mycorrhiza-induced genes, plays an important role in the development, maintenance or functioning of the ECM association and might provide new keys for understanding the positive effects of mycorrhizal symbiosis on host plant nutrition. However, the molecular function, cellular and subcellular localization, regulation and physiological role in the mycorrhiza of this CDF transporter are unknown yet. Hence, MYCOTRANS objectives will be (i) to decipher physiological function, localization, and regulation of the highly mycorrhiza-induced fungal metal transporter by performing a molecular genetics and functional analysis, (ii) to analyze the role of mycorrhiza-induced genes for the fungal symbiosis by developing tools for genome editing (CRISPR/Cas) for the ECM fungus, and (iii) to discover new aspects of mycorrhizal regulation occurring specifically at the level of proteins by the analysis of the ECM proteome and phosphoproteome. To address these objectives, we will use key methodologies which are: (i) heterologous expression in yeast and Xenopus laevis oocytes of the cDNA encoding the metal (putatively Zn, Fe, Mn) transporter of the CDF family, to assess the properties of this transporter, such as its selectivity for several micronutrients; (ii) In situ hybridization and green fluorescent protein (GFP-) fused proteins for cellular and sub-cellular localization of the CDF transporter in yeast and ectomycorrhizae; (iii) production of new CRISPR/Cas vectors and KO fungal mutants to study the role of mycorrhiza-involved fungal genes, as this technique of genome editing will be much more efficient than the RNAi method previously used by Partner 1; (iv) use of an in vitro symbiosis-mimicking system, where the fungus is incubated in a liquid solution either alone or with host plant roots ensuring a cross-talk between both partners of the symbiosis but without the formation of ECM structures on the root; (v) extraction of fungal proteins and separation in three fractions: soluble, microsomal and plasma membrane proteins, to carry out proteome analysis in all protein fractions and phosphoproteome analysis of plasma membrane proteins, as a target of possible post-translational modifications exerted by the host-plant. Establishment of the CRISPR/Cas technique for ECM fungi will lift a technical barrier and provide the scientific community with these missing tools. In addition, the whole set of the expected results should give decisive insights into the actual physiological role of the mycorrhiza-induced genes coding for transport functions, especially those located in the Hartig net that will determine, in turn, the efficiency of the ectomycorrhizal symbiosis. Hence, MYCOTRANS should help us to find true symbiotic marker genes, making it possible to use mycorrhizal interactions for sound management of both croplands and forests taking care of ecosystem services rendered by mycorrhizal fungi.

Processes linking lower and upper parts of the Critical Zone are crucial for sustaining life on continents. Deep roots fulfill essential functions, impacting water and biogeochemical cycles, plant ecophysiology and community ecology, not only in natural forests but also in agrosystems. Rock mineral weathering at depth is expected to be an essential source of nutrients and deep rooted trees are believed to lift water and nutrients that benefit to the whole community. However, quantifying this nutrient lift remains a challenge, linked on the one hand to the hidden nature of the roots and on the other hand to the complexity of the rhizosphere. The Nutrilift project will take up the challenges of understanding and quantifying the role of nutrient lift in the functioning of the Critical Zone, guided by the hypothesis that while in natural forests, deep-rooted species can derive some of their nutrient resources from increased mineral weathering at depth. The relative importance of this process in agrosystems is much lesser, whereas agroforestry systems represent an intermediate situation. Conducted at the International Research Laboratory CEFIRSE (IRD-CNRS-INRA-UPS, Indian Institute of Science, Bangalore) in close collaboration with our Indian colleagues, the project will build on the long-term monitoring of the Kabini Critical Zone Observatory, Indian sites of the SNO M-TROPICS (par of OZCAR Research Infrastructure). It will benefit from the exceptional degree of characterization of these sites, where we revealed critical links between surface and depth, in particular the vertical sharing of water resources by the dominant tree species in the forest ecosystem and the importance of accounting for deep uptake for closing biogeochemical cycles. The project will design and implement a new methodological framework for the combined characterization of soil and roots properties and the monitoring of solute and water dynamics from the surface down to great depths for 3 contrasted sites (forest, agroforestry and agriculture). We will use a unique combination of techniques to simultaneously characterize soil and root systems properties from the surface down to the deep regolith and use this information to constrain the hydrological model COMFORT, explicitly accounting for deep root uptake. We will encompass the different processes controlling the storage and mobilization of carbon and nutrients in the rhizosphere with a multiple tool approach, in order to connect the current weathering /nutrient dynamics and the dynamics of root-associated carbon. We will propose a new conceptual model based on intra-plant isotopic budgets to quantify the contributions of the deep regolith to the nutrients uptake. Finally, we will build and use a Reactive Transport Model (coupling COMFORT and WITCH) to simulate the impact of climate change on the Critical Zone functioning and to explore management strategies in a participatory approach with stakeholders. By quantifying the impact of coupling/decoupling the “invisible and visible biosphere” on nutrient cycles, the project will allow a better assessment of ecosystem’s resilience and to design more sustainable management practices enhancing biologically mediated Critical Zone processes in agrosystems.

Modern intensive agricultural systems generally focus on the productivity of monocultures. They are characterized by a low diversity of crops, with uniform and symmetrical planting layouts. They largely rely on the utilization of chemical inputs. They are widely denounced for their negative environmental impacts. In this context, the ecological intensification framework proposes to use exploit biodiversity in order to better achieve, such ecosystem services and soil conservation. Intercropping, i.e. the simultaneous growth of two or more crops mixed in the same field, appears to have the potentialities to improve the productivity, resilience capacity and ecological sustainability of agrosystems through the intensification of such positive interactions between plants as facilitation and niche complementarity. Cereal-legume intercropping turns out to be effective in low N agrosystems since legumes have the ability to fix atmospheric nitrogen via their symbiosis with rhizobia. This fixed N in turn benefits to the cereal through various ecological processes. The objective of the project is to improve the benefit of legumes for intercropped cereals in low input agrosystems through the management of plant-plant and plant-microbe interactions. The nitrogen fixing symbiosis requires phosphorus and iron to be efficient. While these nutrients are prone to be lacking in N-limited agrosystems as it is the case in Mediterranean agrosystems, plant-plant interactions and plant-microbes (rhizobacteria and mycorrhiza) seem to play an important role for their acquisition, and efficiency in their utilisation. We propose to develop a participatory research project in three Mediterranean agrosystems. Agronomic and environmental diagnosis will be performed on the field to assess N and P biogeochemical cycles as well as Fe availability, in link with the plant performances and the diversity of soil microorganisms. A molecular identification of soil microorganisms from the most productive sites will be done, and a research of genes for tolerance to Fe- and P-deficiencies will be realized. Glasshouse experiments involving various cultivars of cereals and legumes, as well as the beforehand identified microorganisms, will be done in order to disentangle the various mechanisms of nutrient acquisition, sharing and transfer between plants. Other experiments will assessing the effects of cereal-legume-microbe interactions on the development and architecture of the plant root systems and root hair development. These researches are integrated in a strategy of functional ecology on plant-microbe-soil interactions in the low valley of Medjerda at Mateur (Tunisia), Ain Temouchent (Algeria), Haouz (Morocco) and Thessaloniki (Greece). Using multidisciplinary and innovative approaches, the program will provide novel knowledge and understanding of agro-ecosystem management for food production.