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Agroforestry systems associating trees with crops are gaining a growing interest due to their environmental benefits in a context of climate change and biodiversity loss. Still, the impact of trees on the wind dynamics within agroforestry systems remains poorly understood despite the key role played by the wind in energy and mass exchanges, including disease and pest propagation. Here, we present the first detailed analysis of the wind dynamics over agroforestry systems, combining in situ measurements and instantaneous airflow simulations, with a numerical application on spore-like particle dispersion from an infection point source at crop top. Simulations reproduce remarkably well most characteristics of the turbulent wind flow within the agroforestry system. Simulations reveal the presence of two inflection points on the mean wind velocity profile, at crop and tree tops, both inducing the development of mixing-layer type eddies, controlling most of the turbulent exchanges within the agroforestry system. Relative to the local wind, the turbulence at the crop scale is more intense and intermittent in presence of trees. With increasing tree density, the turbulence at crop top becomes dominated by tree-scale motions developing at tree top. The presence of trees has a different impact on particle dispersion according to the particle size and the wind intensity. Trees accentuate the vertical and transversal dispersal of submicron spores while they enhance the short-range deposition of coarser spores on crops, the more as the wind is low, and thus limit the long-range dispersal of coarse spores. Finally, a simple parameterization of the mean wind velocity vertical profile is proposed for agroforestry systems, depending only on the foliage densities and heights of the tree and crop layers. This parameterization leads to an indication of the agroforestry system efficiency to limit spore propagation through an estimation of the Rouse number at crop top.

International audience; Highlights:• The most diversified groups of predatory ants had a significant negative top down effect on CBB infestation.• Higher % of shade favours CBB infestation.• Regulation of CBB depends on the balance between the effects of local (in plot) and global (farm level) variables.• Farmers practices could be efficient to manage CBB and to reduce related damage.• Holistic approach is required to characterize more precisely regulating network in agroforestry systems.Abstract:Pest regulation in agroforestry systems (AFS) is beginning to be well-recognized, but the mechanisms implied in the interaction network between the environment, pests and predators in AFS are still not well-described. The aim of this work is to understand how plant diversity associated with AFS regulates the coffee berry borer (CBB) taking into account a tripartite interaction network: pest–predator–environment. It further seeks to understand how farmers' management practices can modify the regulating network. Using field data from coffee-based AFS and structural equation modeling, we assessed the effects of environmental conditions (% shade cover, tree area surface, coffee density) and farm management (conventional, integrated, organic) on (1) ant predatory groups, (2) the abundance and the damage from CBB and (3) their interactions. Percentage of shade cover was positively correlated to CBB initial infestation (through direct effect) and negatively through its effect on coffee phenology. A higher percentage of shade is also negatively related to damage intensity. Farmers’ practices significantly reduced the CBB population without considerable side effects on the ant predatory group, probably due to the high plant diversity within these farms. The abundance of the most diversified ant predatory group has a top-down effect on the peak of the CBB infestation rate. Our approach appears promising for a better understanding of the complex regulating network in coffee AFS and confirms the importance of an integrated management strategy to reduce CBB damage.

International audience; In complex coffee-based agroforestry systems, quantifying the impact of shade trees on coffee disease regulation and coffee yield is crucial for improving these systems and designing more sustainable ones. To this end, we analyzed interactions amongst shade trees, coffee plants (cv. Catimor), the coffee foliar disease complex and soil characteristics. We studied systems characterized by 40 variables measured in 60 plots located on three farms (monitored for 2 years) in Nicaragua. These variables characterized six system components grouped in six statistical blocks: shade trees (shade percentage and species abundancy), soil characteristics (fertility), foliar diseases, coffee plant characteristics (age and size), coffee growth and yield. We used partial least square path modelling (PLS-PM), i.e. a structural equation modelling approach used to understand and quantify interactions between the six blocks. Shade trees (mostly the associated shade percentage) had direct positive effects on foliar disease severity and incidence and soil quality, while having negative effects on coffee growth and yield. Soil characteristics (carbon, nitrogen, litter index, water infiltration potential) were negatively correlated with foliar diseases. An excessive shade percentage then had an indirect negative effect on coffee growth and yield due to the increased prevalence of foliar diseases. Finding the optimal shade cover can help reduce foliar diseases and enhance coffee berry production. The 'dose effect' of shade cover must also be considered because excessive shade, as well as lack of shade, have negative impacts on coffee growth and yield. Overall, effective shade management requires an analysis of trade-offs between soil quality, disease regulation and yield gains. In conclusion, PLS-PM turned out to be a good tool for studying agroecosystem networks and enabled us to put forward some foliar disease management and coffee yield enhancement guidelines.

The combined and interacting effects of land-use change, resource extraction and climate change threaten the sustainability of millions of mainly smallholder farms in tropical agroforested landscapes. In many of these landscapes, coordinated action among stakeholders at landscape level would help to address challenges such as pests and diseases, price crises and climate change. However, methods to facilitate the co-production of sustainable landscape management in such complex multi-stakeholder systems are currently largely lacking. In this paper, we present a novel approach to explore pathways for the sustainability transition of agroforestry systems. By combining participatory forecasting and backcasting approaches, based on serious games and future vision development, we explore relevant agroforestry management strategies for reaching sustainable future coffee-based agroforestry landscapes. We focused our research on the challenges faced in the main coffee-producing area in Nicaragua. Here, we organized five participatory game sessions to explore farmer decision-making processes, farming strategies and to develop new networks and stimulate social learning among farmers. In the associated backcasting workshop, the most influential game session participants joined technicians, researchers and municipality officials to collectively envision sustainable future landscape management. In all game sessions, farmers developed diversified coffee-based agroforested landscapes characterised by increased density and diversity of shade trees, for the purpose of income diversification as well as forest conservation. During the backcasting workshop, the participants identified policy instruments and community-based solutions for the transition to sustainable landscapes. Our participatory approach facilitated discussion on landscape planning among farmers and other stakeholders and allowed the outline of a pathway towards the collective envisioned future landscape. The combination of participatory forecasting and backcasting proved to be a helpful tool to support multi-stakeholder processes towards sustainable landscape management in this and other complex landscapes.

Assessment of crop loss due to multiple diseases and pests (D&P) is a necessary step in designing sustainable crop management systems. Understanding the drivers of D&P development and yield loss helps identify leverage points for crop health management. Crop loss assessment is also necessary for the quantification of D&P regulation service to identify promising systems where ecosystem service provision is optimized. In perennial crops, assessment of crop losses due to D&P is difficult, as injuries can affect yield over years. In coffee, one of the first perennials in which crop loss trials were implemented, crop losses concurrent with injuries were found to be approximately 50% lower than lagged losses that originated following the death of productive branches due to D&P. Crop losses can be assessed by field trials and surveys, where yield reduction factors such as the number of productive branches that have died are quantified, and by modeling, where damage mechanisms for each injury are considered over several years.

The literature on the importance of plant pathogens sometimes emphasizes their possible role in historical foodshortages and even in famines. Aside from such major crises, plant pathogens should also be seen as important reducers of crop performances, with impacts on system sustainability, from the ecological, agronomical, social, and economic standpoints – all contributing ultimately to affecting food security. These views need reconciliation in order to produce a clearer picture of the multidimensional effects of plant disease epidemics. Such a picture is needed for disease management today, but would also be useful for future policies. This article attempts to develop a framework that would enable assessment of the impacts of plant diseases, referred collectively to as crop health, on food security via its components. We have combined three different existing definitions of food security in order to develop a framework consisting of the following six components: (1) Availability. Primary production; (2) Availability. Import - Stockpiles; (3) Access. Physical and supply chain; (4) Access. Economic; (5) Stability of food availability; (6) Utility-Safety-Quality- Nutritive value. In this framework, components of food security are combined with three attributes of production situations: the nature of the considered crop (i.e. food- or non- food), the structure of farms (i.e. subsistence or commercial), and the structure of markets (i.e. weakly organized and local, to strongly organized and globalized). The resulting matrix: [Food security components] × [Attributes of production situations] provides a framework where the impacts of chronic, acute, and emerging plant disease epidemics on food security can be examined. We propose that, given the number of components and interactions at play, a systems modelling approach is required to address the functioning of food systems exposed to plant disease risks. This approach would have application in both the management of the current attrition of crop performances by plant diseases, and also of possible disease-induced shocks. Such an approach would also enable quantifying shifts in disease vulnerability of production situations, and therefore, of food systems, as a result of climate change, globalization, and evolving crop health.

UMR SYSTEM : équipe CONSYST; Intensively managed cropping systems with emphasis on productivity of the main crop can benefit from additional ecosystem services brought by integration of trees in the system − but potential drawbacks must also be accounted for. In an on-farm study, we used a variety of plant, soil and water- related variables to assess the effect of Erythrina spp. and Musa spp. on the provision of ecosystem services in productive, high-quality Coffea arabica plantations in Costa Rica. We found 1) no significant effect of shade trees on coffee production overall; 2) evidence that shade trees do affect flowering and subsequent cherry development, with effects strongly dependent on climate and annual variations in coffee plant physiology; 3) Erythrina shade trees significantly increased soil litter and relative infiltration rate of water in the soil, both linked to soil conservation and decrease in erosion; 4) even in highly fertilized environments, Erythrina trees do fix N which was taken up by adjacent coffee plants. The lack of significant negative effect of shade trees on overall coffee yield and the observation of the provision of other useful services was not unexpected, because of 1) the low density of shade trees in the study site (100–350 trees/ha pruned twice a year on average) and 2) the sensitivity of coffee yields to other interacting effects such as climate, pests and diseases and physiological variations in the plant. Pending further long-term research into the factors affecting coffee yield, we find shade trees provide sufficient ecosystem services to justify their integration in even intensively managed plantations.

The assessment of crop yield losses is needed for the improvement of production systems that contribute to the incomes of rural families and food security worldwide. However, efforts to quantify yield losses and identify their causes are still limited, especially for perennial crops. Our objectives were to quantify primary yield losses (incurred in the current year of production) and secondary yield losses (resulting from negative impacts of the previous year) of coffee due to pests and diseases, and to identify the most important predictors of coffee yields and yield losses. We established an experimental coffee parcel with full-sun exposure that consisted of six treatments, which were defined as different sequences of pesticide applications. The trial lasted three years (2013–2015) and yield components, dead productive branches, and foliar pests and diseases were assessed as predictors of yield. First, we calculated yield losses by comparing actual yields of specific treatments with the estimated attainable yield obtained in plots which always had chemical protection. Second, we used structural equation modeling to identify the most important predictors. Results showed that pests and diseases led to high primary yield losses (26%) and even higher secondary yield losses (38%). We identified the fruiting nodes and the dead productive branches as the most important and useful predictors of yields and yield losses. These predictors could be added in existing mechanistic models of coffee, or can be used to develop new linear mixed models to estimate yield losses. Estimated yield losses can then be related to production factors to identify corrective actions that farmers can implement to reduce losses. The experimental and modeling approaches of this study could also be applied in other perennial crops to assess yield losses.

International audience; Pests and diseases are the main yield-reducing factors in simplified agricultural systems. Their role in complex, diverse, agricultural systems may, however, be less apparent because of the many interactions in which they are involved. However, it is essential to understand the relationships between pests and diseases, on the one hand, and ecosystem services (including crop production), on the other, to develop sustainable agroecosystems. Our study aims to illustrate these complex relationships based on the example of coffee agroecosystems in Costa Rica. We analysed a dataset consisting of 107 coffee plots characterized for their topoclimates, soils, coffee plant production characteristics, cropping practices, and pest and disease injuries. Meta-variables were created through cluster analyses to account for these different broad attributes of coffee-based agroecosystems. In particular, coffee injury profiles were determined on the basis of injury levels incurred by pathogens, nematodes, and insects over the course of one growing season. We used correspondence analysis to assess the levels of linkage between injury profiles and other agroecosystem meta-variables. Indicators of biodiversity based on shade diversity and of attainable yield were incorporated in the analysis as additional variables. Four groups of coffee-based agrosystems were identified, ranging from extensive (low-input, perennial polyculture) to intensive (unshaded high-input monoculture). Each group of coffee-based agroecosystem corresponds to varying levels of pest and disease injuries, crop yield, and ecosystem service provision, excluding coffee production. In each group of coffee-based agrosystem, we discussed the drivers of coffee production and explored potential avenues to improve sustainability based on ecosystem services provision. We highlighted that the physical characteristics of the environment, topoclimate and soil characteristics, are the main drivers of injury profiles and of resulting yield losses. Cropping practices and pest and disease management first need to be adapted to these physical characteristics. Where topoclimate and soils favour pest and disease development, potentially leading to heavy yield losses, system diversification can enhance ecosystem service provision, including production of other crops, thus helping to offset low coffee production. Where physical environmental characteristics hamper pests and diseases, increasing ecosystem service provision by incorporating shade trees may be considered, provided that coffee production is not significantly reduced. We conclude that there is an acute need to quantify losses caused by pests and diseases in agroforestry systems, in order to provide a rational basis for growers' decisions and to better determine the value of economic incentives needed for ecosystem service provision.

International audience; AbstractAgroecosystems represent 38 % of global land use. Agroecosystems are located close to human settlements and are managed to produce food and fibers, traded in markets. Agroecosystems also produce other goods and services essential to human beings, such as climate regulation, flood mitigation, and landscape amenity. Economists and ecologists have developed the ecosystem services framework to foster the provision of these non-commercial services. Scientists can therefore help decision makers to develop sustainable ecosystems by studying ecosystem services. Here, we analyze the trade-offs of ecosystem services of farming systems. We discuss case studies of mixed perennial crops. The set of ecosystem services provided by these agroecosystems depends on their composition, structure, and management. Complex rule-based management will be required if winegrowers are to maintain an adequate set of ecosystem services across contrasting climatic years. Innovations including cover crops in banana systems can fulfill most of the objective set but will rely on increased farm labor. We then discuss the advantages, challenges, and opportunities to include the description of relations between ecosystem services in cropping system design. We propose to extend the yield gap analysis to ecosystem services, as a service gap analysis. This extension faces methodological questions about the potential provision of a service in a region. We conclude on the challenges that need to be faced if we want to use ecosystem services trade-offs to improve the contribution of agricultural systems to human well-being.

International audience; This study was conducted to identify physiological traits associated with cold tolerance in sunflower and to identify the genomic regions involved in their variation. A population of 98 recombinant inbred lines (RILs) and their two parents were sown in the field as usual sowing date (control) and one or two months earlier (long-term low temperature treatments). A trait commonly used to underlying cold tolerance related to the degree of membrane damage, as well as traits associated with growth capacity (chlorophyll content, potential photochemical efficiency of photosystem II and plant dry weight) and finally those reflecting acclimation mechanism to stress conditions (osmotic potential at full turgor, and specific leaf area) have been investigated at early development stages. Significant differences were observed among the three sowing dates for all traits. Chlorophyll content and specific leaf area are genetically associated with cold tolerance. Genetic gains were observed for chlorophyll content and osmotic potential traits in some of early sowing dates, which suggest that they could be used for cold tolerance in breeding programs. QTL analyses show that several putative genomic regions are involved in the variation of the physiological traits studied under low temperature. Major QTLs for cold tolerance associated with SSR markers such as ORS331_2 for the cell membrane stability should be checked in several environments to see if they can be used in marker-assisted selection programs.