Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC

This paper deals with the simulation of microbial degradation of organic matter in soil within the pore space at a microscopic scale. Pore space was analysed with micro-computed tomography and described using a sphere network coming from a geometrical modelling algorithm. The biological model was improved regarding previous work in order to include the transformation of dissolved organic compounds and diffusion processes. We tested our model using experimental results of a simple substrate decomposition experiment (fructose) within a simple medium (sand) in the presence of different bacterial strains. Separate incubations were carried out in microcosms using five different bacterial communities at two different water potentials of −10 and −100 cm of water. We calibrated the biological parameters by means of experimental data obtained at high water content, and we tested the model without changing any parameters at low water content. Same as for the experimental data, our simulation results showed that the decrease in water content caused a decrease of mineralization rate. The model was able to simulate the decrease of connectivity between substrate and microorganism due the decrease of water content

Habitat constraints on the functional significance of soil microbial communities

Habitat constraints on the functional significance of soil microbial communities. EGU 2017, European Geophysical Union General Assembly 201

Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it

Defining Quantitative Targets for Topsoil Organic Carbon Stock Increase in European Croplands: Case Studies With Exogenous Organic Matter Inputs

The EU Mission Board for Soil Health and Food proposed a series of quantitative targets for European soils to become healthier. Among them, current soil organic carbon (SOC) concentration losses in croplands (0.5% yr(-1) on average at 20 cm depth) should be reversed to an increase of 0.1-0.4% yr(-1) by 2030. Quantitative targets are used by policy makers to incentivize the implementation of agricultural practices that increase SOC stocks. However, there are different approaches to calculate them. In this paper, we analyzed the effect of exogenous organic matter (EOM) inputs on the evolution of SOC stocks, with a particular focus on the new European targets and the different approaches to calculate them. First, we illustrated through two case-study experiments the different targets set when the SOC stock increase is calculated considering as reference: 1) the SOC stock level at the onset of the experiment and 2) the SOC stock trend in a baseline, i.e., a control treatment without EOM addition. Then, we used 11 long-term experiments (LTEs) with EOM addition in European croplands to estimate the amount of carbon (C) input needed to reach the 0.1 and 0.4% SOC stock increase targets proposed by the Mission Board for Soil Health and Food, calculated with two different approaches. We found that, to reach a 0.1 and 0.4% increase target relative to the onset of the experiment, 2.51 and 2.61 Mg C ha(-1) yr(-1) of additional C input were necessary, respectively. Reaching a 0.1 and 0.4% increase target relative to the baseline required 1.38 and 1.77 Mg C ha(-1) yr(-1) of additional input, respectively. Depending on the calculation method used, the estimated amounts of additional C input required to reach each quantitative target were significantly different from each other. Furthermore, the quality of C input as represented by the C retention rate of the additional organic material (EOM and crop residue), had a significant effect on the variation of SOC stocks. Our work highlights the necessity to take into consideration the additional C input required to increase SOC stocks, especially for soils with decreasing SOC stocks, when targets are set independently of the baseline

Impact of alley cropping agroforestry on stocks, forms and spatial distribution of soil organic carbon : a case study in a Mediterranean context

UMR SYTEM : Equipe AMPLUS : Analyse et Modélisation du champ cultivé PLUrispécifiqueAgroforestry systems, i.e., agroecosystems combining trees with farming practices, are of particular interest as they combine the potential to increase biomass and soil carbon (C) storage while maintaining an agricultural production. However, most present knowledge on the impact of agroforestry systems on soil organic carbon (SOC) storage comes from tropical systems. This study was conducted in southern France, in an 18-year-old agroforestry plot, where hybrid walnuts (Juglans regia × nigra L.) are intercropped with durum wheat (Triticum turgidum L. subsp. durum), and in an adjacent agricultural control plot, where durum wheat is the sole crop. We quantified SOC stocks to 2.0 m depth and their spatial variability in relation to the distance to the trees and to the tree rows. The distribution of additional SOC storage in different soil particle-size fractions was also characterized. SOC accumulation rates between the agroforestry and the agricultural plots were 248 ± 31 kg C ha− 1 yr− 1 for an equivalent soil mass (ESM) of 4000 Mg ha− 1 (to 26–29 cm depth) and 350 ± 41 kg C ha− 1 yr− 1 for an ESM of 15,700 Mg ha− 1 (to 93–98 cm depth). SOC stocks were higher in the tree rows where herbaceous vegetation grew and where the soil was not tilled, but no effect of the distance to the trees (0 to 10 m) on SOC stocks was observed. Most of the additional SOC storage was found in coarse organic fractions (50–200 and 200–2000 μm), which may be rather labile fractions. All together our study demonstrated the potential of alley cropping agroforestry systems under Mediterranean conditions to store SOC, and questioned the stability of this storage

Modelling dynamic interactions between soil structure and the storage and turnover of soil organic matter

Models of soil organic carbon (SOC) storage and turnover can be useful tools to analyse the effects of soil and crop management practices and climate change on soil organic carbon stocks. The aggregated structure of soil is known to protect SOC from decomposition and, thus, influence the potential for long-term sequestration. In turn, the turnover and storage of SOC affects soil aggregation, physical and hydraulic properties and the productive capacity of soil. These two-way interactions have not yet been explicitly considered in modelling approaches. In this study, we present and describe a new model of the dynamic feedbacks between soil organic matter (SOM) storage and soil physical properties (porosity, pore size distribution, bulk density and layer thickness). A sensitivity analysis was first performed to understand the behaviour of the model. The identifiability of model parameters was then investigated by calibrating the model against a synthetic data set. This analysis revealed that it would not be possible to unequivocally estimate all of the model parameters from the kind of data usually available in field trials. Based on this information, the model was tested against measurements of bulk density, SOC concentration and limited data on soil water retention and soil surface elevation made during 63 years in a field trial located near Uppsala (Sweden) in three treatments with different organic matter (OM) inputs (bare fallow, animal and green manure). The model was able to accurately reproduce the changes in SOC, soil bulk density and surface elevation observed in the field as well as soil water retention curves measured at the end of the experimental period in 2019 in two of the treatments. Treatment-specific variations in SOC dynamics caused by differences in OM input quality could be simulated very well by modifying the value for the OM retention coefficient epsilon (0.37 for animal manure and 0.14 for green manure). The model approach presented here may prove useful for management purposes, for example, in an analysis of carbon sequestration or soil degradation under land use and climate change