Monitoreo de servicios ecosistémicos en un observatorio de cafetales agroforestales. Recomendaciones para el sector cafetalero

Ocho años de estudio de la ecofisiología del café, a través de experimentación y de modelación y el monitoreo de los servicios del ecosistema (SE) en una gran finca cafetalera en Costa Rica, revelaron varias recomendaciones prácticas para los agricultores y los formuladores de políticas. El sistema de cultivo estudiado dentro de nuestro observatorio colaborativo (Coffee-Flux), corresponde a un sistema agroforestal (SAF) a base de café bajo la sombra de grandes árboles de Erythrina poeppigiana (16% de la cubierta del dosel). Una gran cantidad de SE y limitantes dependen de las propiedades locales del suelo (en este caso Andisoles), especialmente de la erosión/infiltración, el agua/carbono y la capacidad de almacenamiento de nutrientes. Por lo tanto, para la evaluación de SE, el tipo de suelo es crucial. Una densidad adecuada de árboles de sombra (bastante baja aquí por la condición de libre crecimiento), redujo la severidad de las enfermedades de las hojas con la posibilidad de reducir el uso de plaguicidas y fungicidas. Un inventario simple del área basal en el collar de las plantas de café permitió estimar la biomasa subterránea y la edad promedio de la plantación, para juzgar su valor de mercado y decidir cuándo reemplazarla. Las fincas de café probablemente estén mucho más cerca de la neutralidad de C que lo indicado en el protocolo actual de C-neutralidad, que solo considera árboles de sombra, no los cafetos ni el suelo. Se proponen evaluaciones más completas, que ncluyen árboles, café, hojarasca, suelo y raíces en el balance C del SAF. Los árboles de sombra ofrecen muchos SE si se gestionan adecuadamente en el contexto local. En comparación con las condiciones a pleno sol, los árboles de sombra pueden (i) reducir la erosión laminar en un factor de 2; (ii) aumentar la fijación de N y el % de N reciclado en el sistema, reduciendo así los requisitos de fertilizantes; (iii) reducir la severidad de enfermedades de las hojas; (iv) aumentar el secuestro de C; (v) mejorar el microclima y (vi) reducir sustancialmente los efectos del cambio climático. En nuestro estudio de caso, no se encontró ningún efecto negativo sobre el rendimiento del café

Development and applications of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer events between bacteria in soil pollutant bioremediation processes

Horizontal gene transfers are critical mechanisms of bacterial evolution and adaptation that are involved to a significant level in the degradation of toxic molecules such as xenobiotic pesticides. However, understanding how these mechanisms are regulated in situ and how they could be used by man to increase the degradation potential of soil microbes is compromised by conceptual and technical limitations. This includes the physical and chemical complexity and heterogeneity in such environments leading to an extreme bacterial taxonomical diversity and a strong redundancy of genes and functions. In addition, more than 99 % of soil bacteria fail to develop colonies in vitro, and even new DNA-based investigation methods (metagenomics) are not specific and sensitive enough to consider lysis recalcitrant bacteria and those belonging to the rare biosphere. The objective of the ANR funded project “Emergent” was to develop a new culture independent approach to monitor gene transfer among soil bacteria by labeling plasmid DNA with magnetic nanoparticles in order to specifically capture and isolate recombinant cells using magnetic microfluidic devices. We showed the feasibility of the approach by using electrotransformation to transform a suspension of Escherichia coli cells with biotin-functionalized plasmid DNA molecules linked to streptavidin-coated superparamagnetic nanoparticles. Our results have demonstrated that magnetically labeled cells could be specifically retained on micromagnets integrated in a microfluidic channel and that an efficient selective separation can be achieved with the microfluidic device. Altogether, the project offers a promising alternative to traditional culture-based approaches for deciphering the extent of horizontal gene transfer events mediated by electro or natural genetic transformation mechanisms in complex environments such as soil

“Faidherbia-Flux”: adapting crops to climate changes in a semi-arid agro-sylvo-pastoral open observatory (Senegal)

National audienceThe adaptation of semi-arid crops to climate changes is theoretically possible through agroforestry, provided that the trees exert little competition, or even increase the multifunctional LER (LER_M). We monitored microclimate, net primary productivity (NPP), CO2 and H2O fluxes in a semiarid agro-sylvo-pastoral system (Niakhar, Senegal), dominated by the multipurpose Faidherbia albida (FA) tree. Undercrops were mainly millet and peanut, under annual rotation. We scanned a 1.24 ha millet under FA plot with UAV photogrammetry in RGB, thermal infrared and multispectral bands. At harvest, we collected 12 subplots of 15 millet holes each, distributed either below the crown of FA, or at 2.5 x crown radius, or at 5 x crown radius. We separated all organs. The whole millet root system (0-200 cm) was sampled also in 2 m trenches, totalizing 4 millet holes, where all roots were sorted by layer. The whole plot harvest will allow extrapolating yield from subplots, through UAV images. Millet yield per unit ground area was about 3 times higher below FA, with still a positive influence at 2.5 x crown radius and less impacts of pests close to FA. In the trenches, we noted higher soil humidity and SOC close to the FA trunks. This observatory is open for collaboration

Measuring and modelling energy partitioning in canopies of varying complexity using MAESPA model

Evapotranspiration and energy partitioning are complex to estimate because they result from the interaction of many different processes, especially in multi-species and multi-strata ecosystems. We used MAESPA model, a mechanistic, 3D model of coupled radiative transfer, photosynthesis, and balances of energy and water, to simulate the partitioning of energy and evapotranspiration in homogeneous tree plantations, as well as in heterogeneous multi-species, multi-strata agroforests with diverse spatial scales and management schemes. The MAESPA model was modified to add (1) calculation of foliage surface water evaporation at the voxel scale; (2) computation of an average within-canopy air temperature and vapour pressure; and (3) use of (1) and (2) in iterative calculations of soil and leaf temperatures to close ecosystem-level energy balances. We tested MAESPA model simulations on a simple monospecific Eucalyptus stand in Brazil, and also in two complex, heterogeneous Coffea agroforests in Costa Rica. MAESPA satisfactorily simulated the daily and seasonal dynamics of net radiation (RMSE = 29.6 and 28.4 W m−2; R2 = 0.99 and 0.99 for Eucalyptus and Coffea sites respectively) and its partitioning between latent-(RMSE = 68.1 and 37.2 W m−2; R2 = 0.87 and 0.85) and sensible-energy (RMSE = 54.6 and 45.8 W m−2; R2 = 0.57 and 0.88) over a one-year simulation at half-hourly time-step. After validation, we use the modified MAESPA to calculate partitioning of evapotranspiration and energy between plants and soil in the above-mentioned agro-ecosystems. In the Eucalyptus plantation, 95% of the outgoing energy was emitted as latent-heat, while the Coffea agroforestry system’s partitioning between sensible and latent-heat fluxes was roughly equal. We conclude that MAESPA process-based model has an appropriate balance of detail, accuracy, and computational speed to be applicable to simple or complex forest ecosystems and at different scales for energy and evapotranspiration partitioning

Suivi des services écosystémiques dans un observatoire de caféiers agroforestiers. Applications pour la filière du café

Chapitre 2National audienceEight years of studying coffee ecophysiology and monitoring ecosystem services (ES) in a large coffee farm in Costa Rica revealed several practical recommendations for farmers and policy makers. The cropping system studied within our collaborative observatory (Coffee-Flux) corresponds to a coffee-based agroforestry system (AFS) under the shade of large trees of Erythrina poeppigiana (16 % of canopy cover). A lot of ES and disservices depend on local soil properties (here Andisols), especially erosion/infiltration, water/carbon and nutrient storage capacity. Therefore, for ES assessment, the type of soil is crucial. An adequate density of shade trees (rather low here) reduced the severity of leaf diseases with the prospect of reducing pesticide-fungicide use. A simple inventory of the basal area at collar of the coffee plants allowed estimating the belowground biomass and the average age of the plantation, to judge of its market value and to decide when to replace it. Coffee farms are probably much closer to C neutrality than predicted by the current C-Neutral protocol, which only considers shade trees. More comprehensive assessments, including trees, coffee, litter, soil, and roots in the C balance of the AFS are proposed. Shade trees offer many ES if they are adequately managed in the local context. As compared to full sun conditions, shade trees may (i) reduce laminar erosion by a factor of 2, (ii) increase N2 fixation and the % of N recycled into the system, thus reducing fertilizer requirements, (iii) reduce the severity of leaf diseases, (iv) increase C sequestration, (v) improve the microclimate, and (vi) substantially reduce the effects of climate change. In our case study, no negative effect on coffee yield was found.Huit ans de travaux de recherche sur les services écosystémiques dans une grande ferme caféière du Costa Rica (observatoire collaboratif Coffee-Flux, en système agroforestier à base de caféiers sous de grands arbres d'Erythrina poeppigiana, surface projetée de couronne de l'ordre de 16 %) ont suggéré plusieurs applications pour les agriculteurs et les décideurs. Il est apparu que de nombreux services écosystémiques dépendaient des propriétés du sol (ici des Andisols), en particulier de l'érosion, de l'infiltration, de la capacité de stockage de l'eau et des éléments nutritifs. Nous confirmons qu'il est essentiel de lier les services hydrologiques et de conservation au type de sol en présence. Une densité adéquate d'arbres d'ombrage (plutôt faible ici) permet de réduire la sévérité des maladies foliaires avec, en perspective, une réduction de l'usage de pesticides-fongicides. Un simple inventaire de la surface basale au collet des caféiers permet d'estimer la biomasse souterraine et la moyenne d'âge d'une plantation de caféiers, ce qui permet d'évaluer sa valeur marchande ou de planifier son remplacement. Le protocole de calcul actuel pour la neutralité carbone des systèmes agroforestiers ne prend en compte que les arbres d'ombrage, pas la culture intercalaire. Dans la réalité, si on inclut les caféiers, on se rapproche très probablement de la neutralité. Des évaluations plus complètes, incluant les arbres, les caféiers, la litière, le sol et les racines dans le bilan en carbone du système agroforestier sont proposées. Les arbres d'ombrage offrent de nombreux servies écosystémiques s'ils sont gérés de manière adéquate dans le contexte local. Par rapport aux parcelles en plein soleil, nous montrons qu'ils réduisent l'érosion laminaire d'un facteur 2, augmentent la fixation de l'azote (N2) atmosphérique et le pourcentage d'azote recyclé dans le système, réduisant ainsi les besoins en engrais. Ils réduisent aussi la sévérité des maladies foliaires, augmentent la séquestration de carbone, améliorent le microclimat et atténuent substantiellement les effets des changements climatiques. Dans notre étude de cas, aucun effet négatif sur le rendement n'a été enregistré