Emergent properties of soil microbial functions: Upscaling from 3D modeling and spatial descriptors of pore scale heterogeneity – Soilµ-3D

Many models exist that describe the emission of greenhouse gases such as CO2 and N2O from soils. However, these global models need improvements to yield more accurate predictions. Indeed these models are ignoring important microscopic aspects of soils, in particular their high level of heterogeneity at the microbial habitat and pore scale, caused by soil structure which can lead to a spatial disconnection between soil carbon and nitrogen, oxygen and the microrganisms. Micro-scale processes that occur within the pores in soils affect phenomena at much larger spatial and temporal scales. New inputs and parameters are needed for the soil compartment in the global “circulation” models used by climatologists to predict future climate patterns.
Most microbial degradation models developed in soil science use empirical functions, also called “reduction functions”. They take into account the different environmental factors that affect microbial functions such as biodegradation, denitrification or nitrification. Among these different factors, those linked to temperature and water content are conventionally used and accepted. However this type of approach cannot describe well the complex interactions that occur between processes. Therefore, such interactions need to be better represented in biogeochemical models for more reliable simulations. A recent alternative approach to the simulation of microbial degradation of organic matter is the "Bottom-Up" approach, based on an explicit description of the soil pore space at the small scale, that of the microbial habitats, and of the processes taking place therein. Innovative modeling tools have been developed at scales directly relevant to microorganisms. Emergence can be captured from the diversity of scenarios that can be run from these models and that would have been much more laborious to carry out experimentally. In parallel with the development of these 3D sophisticated models, technological advances have been made in the 3D visualization at the microscale. The Bottom-Up approach faces limitations due to the computational cost of describing the 3D heterogeneities of the soil at the µm scale to produce output at the centimeter column scale. Upscaling methods have been applied in the area of hydrology mainly to upscale water or solute transport properties taking into consideration the porous structure. However averaging methods used in soil physics or hydrology eliminate information that, in some situations like those involving microorganisms, appears essential. One of the challenges is to find a way to bring the micro-heterogeneities registered at the µ-scale to the soil profile using modeling and especially models of intermediate complexity between pore scale 3D models and existing field models. Revisiting upscaling methodology for soil microbial functions are essential to build more accurate soil models of microbial functions.
Our previous MEPSOM project (ANR, 2009-2013) showed how soil physical characteristics control the decomposition of organic substrates. It has developed a suite of methods and models to visualize in 3D soil heterogeneity at scales relevant for microorganisms. 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. In Soilµ-3D project, MEPSOM’s 3D models will pass the baton to simpler models able to run at the field scale for a better prediction of organic matter decomposition, nitrous oxide emission and organic pollutants impacted by climate and environmental changes. The general question we intend to answer in the proposed research is whether information on the spatial heterogeneity of soils at the microscale can be used to predict the processes observed at the macroscale in soils.