MIOR: an individual‐based model for simulating the spatial patterns of soil organic matter microbial decomposition

Abstract

An individual-based model, called MIOR, was designed to assess hypotheses on the effect of the spatial distribution of organic matter and microbial decomposers on soil carbon and nitrogen dynamics. Two main types of object were defined to represent the decomposers and the soil organic substrates. All these objects were positioned in a 3D space. The exchange of carbon and nitrogen between these various entities was simulated. Two scenarios were tested according to the degrees of clustering of organic matter and of microorganisms. The results of simulations highlighted the effect of the ratio of accessible organic carbon to microbial carbon on the dynamics of microbial biomass and CO 2 release. This ratio was determined by the number of contacts between one object representing the microbial decomposers and the surrounding objects representing the organic substrates.MIOR: modèle individu-centré de simulation de la distribution spatiale des processus microbiens de la décomposition des matières organiques dans les sols Résumé Un mode`le individu-centre´, appele´MIOR, a e´te´conc xu pour tester les hypothe`ses concernant les effets de la distribution spatiale des matie`res organiques et des microde´composeurs dans les sols sur la dynamique du carbone et de l'azote mine´ral. Deux principaux types d'objets ont e´te´de´finis repre´sentant les microorganismes de´composeurs et les substrats organiques. Ces objets sont positionne´s dans une espace a`trois dimensions. Les e´changes de carbone et d'azote entre ces deux entite´s sont simule´s. Deux sce´narios sont teste´s selon des niveaux d'agre´gation des microorganismes et celui des matie`res organiques. Les re´sultats des simulations mettent en avant l'importance de la quantite´de carbone organique accessible par unite´de carbone microbien sur la dynamique de la biomasse microbienne et du CO2 de´gage´. Cette quantite´est de´termine´e par le nombre de contacts entre un objet repre´sentant des microde´composeurs et des objets qui l'entourent repre´sentant les substrats organiques.

Investigating microbial transformations of soil organic matter: synthesizing knowledge from disparate fields to guide new experimentation

“…Coarsely, models of SOM decay can be grouped into two categories: those that are spatially explicit, and those that implicitly treat the factors influencing SOM decay as spatially homogeneous. The first category comprises models such as reactive transport models, often invoked by engineers or hydrologists (Masse et al, 2007;Scheibe et al, 2009), while the second category is more familiar to ecologists (Schimel and Weintraub, 2002;Allison, 2005;Allison et al, 2010;Davidson et al, 2012;Manzoni et al, 2012a;Moorhead et al, 2012;Moyano et al, 2013 The literature values for apparent E a are shown at the pH at which the reaction was actually observed, and does not necessarily correspond to the pH of the soils from which the samples were taken. See Sect.…”

“…There are two approaches widely employed in other fields that could be used for coarse graining SOM dynamics. One is to start with individual dynamics, as in Masse et al (2007), and then derive the dynamics of the aggregate, in this case the entire soil profile, from the individual level dynamics. Durrett and Levin (1994) refer to this as deriving a hydrodynamic limit because of the analogous derivation of Navier-Stokes equations from the mass transfer for individual parcels of liquid.…”

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

“…In previous version of our model (Monga et al, 2008), we modelled organic matter decomposition using an offer-demand approach (Masse et al, 2007). We assumed that, depending on the minimum values of the degradation rate of solid organic matter or microbial growth rate (both expressed in C units), one of these two kinetics was dominating the decomposition rate.…”

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data

“…Among them, lattice-Boltzmann models (LBM) [29,20] are able to describe water, solute, and particulate transport in the interstitial space of soils, as well as the shape of air-water interfaces [13,53], without having to invoke the kind of simplifying assumptions about the geometry or topology of soil pores that were typical of earlier generations of models, based on traditional partial differential equations or capillary network idealizations. Similarly, agent-or individual-based models describe quantitatively the growth and metabolism of microorganisms much more realistically than traditional models, based on descriptions of population dynamics, and are able to account in great detail for the effects of the relative spatial distributions of fungi [13], bacteria [27,30,18,15], and the organic matter on which they feed. At the moment, the development of each of these different models is moving forward, in parallel with interdisciplinary efforts to combine them in order to describe various types of micro-scale scenarios and assess the nature of emergent properties of soil systems [13].…”