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.

Savannas and tropical grasslands represent about 25% of terrestrial ecosystems. In humid savannas, primary productivity can be as high as in tropical rain forests, although savannas are extremely constrained by fire, herbivory, rainfall seasonality and nutrient-poor soils. Such paradoxically high productivity may be partly due to the capacity of perennial grasses (Poaceae) to inhibit nitrification (actually its first step: oxidation of ammonia to nitrite), a process called Biological Nitrification Inhibition (BNI). By limiting the production and thus possible losses of nitrate, BNI leads to more nitrogen (N)-conservative ecosystems. So far, it is not known (i) how common such a capacity is among tropical grasses across the globe, and (ii) whether BNI only inhibits bacterial ammonia oxidizers or also archaeal ammonia oxidizers, and how BNI affects nitrifiers at the activity, abundance and diversity levels. Further, (iii) by limiting nitrate production, BNI could also decrease denitrification and N2O emissions, a potent greenhouse gas, but this remains to be studied. Last, (iv) whether BNI abilities of tropical grasses could be used in agroecology approaches and allow a better maintenance of soil N fertility under low fertilizer inputs in tropical agroecosystems remains to be explored. Our project thus aims at answering the following questions: (1) What is the occurrence of BNI ability among tropical savanna grasses across the globe? Is this ability correlated to particular environmental constraints? (2) What are the mechanisms underlying BNI, i.e. its impacts on soil microbial communities, in particular nitrifier groups, and BNI feedbacks to plants? (3) Can BNI-grasses be used as cover crop to increase agriculture sustainability? (4) What is the impact of BNI on the N budget of tropical (agro)ecosystems? The project is based on collaborations already initiated through two international consortia (an International project on savannas funded by the Belmont Forum, and the BNI International Consortium) led by two of the project partners. It combines multiple disciplines (savanna ecology, plant physiology, microbial ecology, agroecology and agronomy, biogeochemistry) and several approaches: the in situ and common garden screening of BNI capacities of savanna grasses; the analysis in greenhouse experiments of the mechanisms underlying BNI in terms of plant-soil microorganisms relationship; an agroecological proof-of-concept experiment using perennial BNI-grasses as cover crop; and the modelling of the role of BNI on N dynamics in tropical (agro)ecosystems. Importantly, the complementary skills of project partners and complementary approaches are well integrated within the project. The expected impacts of the project range from (1) a strong academic impact about the relationships between BNI-grasses, soil microbial communities and N cycling in tropical savannas of the world (i.e. breakthrough concerning the understanding of the environmental drivers favorable to and mechanisms underlying BNI ability) to (2) the assessment of the interest of grasses with high BNI capacities to the design of innovative, N-conservative agricultural systems (breakthrough for agroecology which could have major societal outcomes on a longer term). The success of the project will be maximized by the fact that (1) it gathers key expertise (the project PI has discovered BNI; the Japanese Partner has discovered the molecular mechanism of BNI; the LEM partner has discovered biological control on denitrification and its molecular mechanism); (2) the project will build on an already established network of savanna scientists who have agreed to provide samples for the worldwide scanning of BNI-grass capabilities; (3) two French teams have been working for 20 years in Ivory Coast, and collaborated with the team from Ivory Coast; and (4) three CGIAR centers are part of the international BNI consortium.

The effects of increasing global temperatures on soil biodiversity and the resulting effects on the coupling/decoupling of biogeochemical C, N, P cycles are poorly understood. This project attempt to assess the biodiversity and functional composition of soil microbial communities, including soil fauna (earthworms) and plant-soil interactions responses to soil warming using three whole soil warming experiments established in France, USA and China. We will focus our study on whole soil profiles, as in particular subsoil horizons may have a large temperature response to warming and could release carbon to the atmosphere as positive feedback mechanism. The information obtained through the data generated by our project will be used to benchmark an existing simulation model, which includes representation of soil depth, transport, and microbial physiology of functional guilds. The simulations outcomes can then support the formulation of policies to promote adaptation and mitigation strategy.