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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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The reduction of greenhouse gas (GHG) emissions by improving the efficiency of agricultural systems through robust ecologically-based management practices represents the most important challenge facing agriculture today. Models are needed to evaluate the effects of soil properties, climate, and agricultural management practices on soil carbon and on the nitrogen transformations responsible for GHG emissions. Models of Carbon and nitrogen cycles in soils like RothC, Century, or CERES need improvements so they can provide more accurate and robust predictions. They use empirical functions which account for the different environmental factors that affect microbial functions. However, these types of function have limitations because i) they don’t consider the micro heterogeneity of soil at the scale of microorganisms and ii) they cannot describe processes that are connected to each other by complex interactions linked to soil structure. Mechanistic representation of small-scale processes was identified in literature as one of the priorities to improve these global soil organic matter dynamics models.

Our MEPSOM project (ANR, 2009-2013) showed the importance of the habitat of soil microorganisms, and especially how physical characteristics (pore sizes, connectivity) control the decomposition of organic substrates via experimental microcosm. MEPSOM project has developed a suite of methods and models to visualize in 2D or 3D soil heterogeneity at scales relevant for microorganisms. It has also contributed successfully to the development of three very complementary 3D models able to simulate for the first time the microbial degradation of organic matter at the scale of microhabitats in soil using real 3D images of soils. The goal of this new project is now to go further by using the 3D models resulting from MEPSOM to upscale heterogeneities identified at the scale of microhabitats to the soil profile scale. The aims of the project are to: develop new descriptors of the pore scale 3D soil heterogeneity that explain the fluxes measured at the core scale, use our 3D models to connect the µ-scale heterogeneity and the measured macroscale fluxes, develop new simple models describing the soil micro-heterogeneity and integrating these micro-features into field-scale models.

The originality of our approach is to bring together scientists from soil science and scientists from applied mathematics and modeling. The interaction between these two populations of researchers will break with traditional modeling formalisms used in soil science.

To start the project, partners will meet to establish and carry out scenarios from existing models of MEPSOM project. This first step will further define strategic experiments for measuring the emissions of CO2 and N2O under different micro-environmental conditions in WP1. 3D images of  the pore-scale distribution of water, particulate organic matter, and microorganisms will be produced in WP2 from the samples provided by WP1. Descriptors of heterogeneity will also be calculated on these 3D images. The 3D pore scale models will upscale the 3D pore scale heterogeneity and simulate global CO2 and N2O fluxes at the core scale that could be tested against experimental data of WP1. Simulation scenarios exploring contrasted micro-environmental conditions will be carried out from these 3D models inWP3. Correlation between the descriptors calculated at the pore scale and the gas fluxes simulated at the core scale will serve as a basis for the production of functions or simple models which will relay the information to bring the microscopic heterogeneity to the soil profile. WP 5 will propose improvements in the models describing the process at field scale and a test of these improvements with existing field data.


La réduction des émissions de gaz à effet de serre (GES) représente un défi majeur auquel doit faire face l'agriculture aujourd'hui.

Les modèles décrivant le cycle du carbone et de l'azote dans les sols (RothC, Century, CERES…) permettent d’évaluer l’effet des propriétés du sol, du climat et des pratiques agricoles sur des émissions de GES mais ils ignorent les processus microscopiques du sol. Afin que ces modèles fournissent des prévisions plus précises et robustes, la représentation mécaniste des processus à petite échelle se révèle essentielle

Le projet Soilµ3D – Propriétés émergentes des fonctions microbiennes dans les sols : Identification de descripteurs spatiaux de la structure du sol à partir de modélisations 3D à l'échelle des habitats microbiens, a pour ambition d’utiliser les modèles de simulation de la dégradation microbienne de la matière organique à l'échelle des micro-habitats à l'aide d’images 3D du sol pour porter les hétérogénéités identifiées à l'échelle des micro-habitats aux échelles du profil de sol.

Coordonné par Patricia Garnier, UMR Écologie fonctionnelle et écotoxicologie des agroécosystèmes (Inra, AgroParisTech), Soilµ3D a été sélectionné dans le cadre de l’appel à projets générique - Gestion sobre des ressources et adaptation au changement climatique de l’Agence nationale de la recherche. Les résultats ont été publiés le 24 juillet 2015.

Soilµ3D, trois objectifs en lien avec le changement climatique

Le projet Soilµ3D a pour objectif de

  • développer de nouveaux descripteurs de l’hétérogénéité 3D du sol à l’échelle des pores qui expliquent les flux mesurés à l'échelle supérieure centimétrique ;
  • utiliser des modèles 3D pour faire un lien entre l'hétérogénéité visualisée à l’échelle microscopiques et les flux mesurés à l’échelle macroscopiques ;
  • développer de nouveaux modèles décrivant ces micro-hétérogénéités et les porter dans les modèles développés à l’échelle du champ.

Soilµ3D est structuré en cinq ensembles de taches (WP).

La réalisation de scénarios, à partir des modèles du projet MEPSOM, permettra de définir de nouvelles stratégies expérimentales pour mesurer les émissions de CO2 et N2O dans différentes microenvironnements (WP1). Les échantillons prélevés sur différentes parcelles agricoles permettront de produire les images 3D, dans les pores du sol, de la distribution de l’eau, des matières organiques et des micro-organismes (WP2). Les descripteurs de l’hétérogénéité seront calculés à partir de ces images. Des modèles 3D développés à l'échelle des pores, feront le lien entre la visualisation 3D microscopiques et les flux mesurés aux échelles macroscopiques. Des scénarios de simulations explorant les conditions contrastées de micro-environnements seront réalisés à partir de ces modèles  (WP3). Les corrélations entre les descripteurs, établis à l'échelle des pores et les flux de gaz, simulés à l'échelle centimétrique serviront de base pour produire des fonctions ou des modèles simples qui feront passer les informations des hétérogénéités microscopiques jusqu’au profil du sol (WP4). Enfin, WP 5 proposera d’améliorer les modèles mis en œuvre à l'échelle du champ et de les tester avec des données de terrain.

Grâce à des technologies avancées, ce projet permettra d’améliorer nos connaissances et aussi les modèles de prédiction des émissions de gaz à effet de serre.  Ces modèles serviront à l’identification de scénarios qui permettent à l’agriculture de limiter les émissions de gaz à effet de serre et de séquestrer d’avantage de carbone.