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

Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils

Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil‐atmosphere exchange of greenhouse gases

Over the last two decades, the fact that soils are significant sources of greenhouse gases (GHG), e.g., carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and water vapor, has received considerable attention from the scientific community. Many laboratory and field experiments have been carried out to investigate the release of GHG by soils, and a wide range of computer modeling approaches have been explored to encapsulate what is known about the process, as well as to improve its prediction at various spatial and temporal scales

Numerical simulations of isoproturon transport in conventional soil cultivation with compost obtained by urban biological waste recycling

Strukturna heterogenost tla uzrokovana agrotehničkim zahvatima može imati veliki utjecaj na tok vode i pronos tvari. Glavni cilj rada je bio procijeniti kako prisustvo različitih strukturnih zona u obradivom sloju tla utječe na iniciranje preferencijalnih tokova vode u tlu te procijeniti utjecaj degradacije herbicida izoproturona na dinamiku njegova pronosa. Dugogodišnji podatci s poljskog pokusa (QualiAgro, 2004. – 2010.) na kojem se vrši primjena komposta dobivenog recikliranjem urbanog bio-otpada korišteni su za kalibraciju i verifikaciju numeričkog modela HYDRUS-2D. Tok vode i dinamika izoproturona uspješno su simulirani nakon kalibracije hidrauličkih parametara i temporalne optimizacije brzine degradacije izoproturona. Preferencijalni tokovi su inicirani u međubrazdama uslijed velike poroznosti nastale dodatkom komposta, a kao posljedice usmjeravanja toka okolo zbijenih zona tla. S druge strane, dodatak komposta dobiven recikliranjem kanalizacijskog mulja i zelenog bio-otpada povećao je degradaciju i sorpciju izoproturona u zonama koje su sadržavale najveće količine komposta te se posljedično smanjio i njegov pronos.The structural soil heterogeneity caused by agro-technical measures can have a large impact on water flow and sediment transfer. The main objective of the paper was to evaluate how the presence of different structural zones in the soil’s arable layer affects the initiation of preferential water flows in the soil and to assess the impact of the herbicide isoproturon degradation rate on the dynamics of its transport. Long-period data from the Polish trial (QualiAgro, 2004 - 2010) which applies compost obtained through urban biological waste recycling were used for the calibration and verfication of the numerical model HYDRUS-2D. Water flow and isoproturon dynamics were successfully simulated after the calibration of hydraulic parameters and temporal optimization of the isoproturon degradation rate. Preferential flows occured in interfurrows due to a high compost porosity resulting from the flow’s direction around the soil’s compacted zones. On the other hand, the addition of compost obtained through recycling of sewage sludge and green biological waste increased isoproturon degradation and sorption in areas containing the highest compost amounts, thus reducing its transport

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Emergent properties of microbial activity in heterogeneous soil microenvironments:Different research approaches are slowly converging, yet major challenges remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gases. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale). For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. In terms of microbial aspects, whereas a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because relevant experimental data are extremely scarce. For the overall research to move forward, it will be crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead

Lessons from a landmark 1991 article on soil structure: distinct precedence of non-destructive assessment and benefits of fresh perspectives in soil research

In 1991, at the launch of a national symposium devoted to soil structure, the Australian Society of Soil Science invited Professor John Letey to deliver a keynote address, which was later published in the society’s journal. In his lecture, he shared the outcome of his reflexion about what the assessment of soil structure should amount to, in order to produce useful insight into the functioning of soils. His viewpoint was that the focus should be put on the openings present in the structure, rather than on the chunks of material resulting from its mechanical dismantlement. In the present article, we provide some historical background for Letey’s analysis, and try to explain why it took a number of years for the paradigm shift that he advocated to begin to occur. Over the last decade, his perspective that soil structure needs to be characterised via non-destructive methods appears to have gained significant momentum, which is likely to increase further in the near future, as we take advantage of recent technological advances. Other valuable lessons that one can derive from Letey’s pioneering article relate to the extreme value for everyone, even neophytes, to constantly ask questions about where research on given topics is heading, what its goals are, and whether the methods that are used at a certain time are optimal

Assessing the multiple effects of dissolved organic matter on the transport of organic pollutants in subsoil horizons through a modular modeling approach

International audienceThe role of dissolved organic matter (DOM) in the transport of trace organic pollutants through the soil profile remains controversial. Several studies reported enhanced transport for nonpolar pesticides and other pollutants such as pharmaceuticals (e.g., Borgman & Chefetz 2013). It is generally hypothesized that DOM modifies the sorption properties of the contaminants through cosorption and/or cumulative sorption (Totsche et al. 1997). Co-transport with DOM can also enhance the mobility of pollutants (Chabauty et al. 2016). Other authors reported little effect of DOM on both sorption or desorption of herbicides (e.g., Barriuso et al. 2011). To help elucidating the multiple roles of DOM, we developed the PolDOC model implemented in the VSoil modeling platform of INRAE. We took advantage of the modularity of the platform to couple available 1D water flow and solute transport models with novel reactivity modules for organic pollutants and DOM. Indeed, sink/source terms in the transport equation have been used to calculate the interactions between pollutants, DOM and the soil solid phase.The model was designed to simulate the transport of organic pollutants in intact soil cores sampled in the Bt horizon of a cultivated Albeluvisol to which either a synthetic soil solution without DOM (SYNTH), a soil solution extracted from the top horizon (CONTROL) or a soil solution extracted from the top horizon of a neighbour plot receiving sewage sludge and green waste compost (SGW) were applied (Chabauty et al., 2016). In PolDOC, the organic pollutants can be transported either free or associated with DOM. To describe the multiple roles of DOM in the transport of organic pollutants we first simplified the wide spectrum of organic molecules which constitute DOM and distinguished two types of DOM with different reactivity: DOMBt produced by depolymerization of the organic matter in the Bt soil horizon, and DOMSURF, produced by depolymerization of the organic matter of the surface horizon.The model was used to simulate the transport of both DOM types and three different organic pollutants: isoproturon (ISO), a mobile herbicide, epoxiconazole (EPX), a moderately mobile fungicide and sulfamethoxazole (SMX), a mobile antibiotic. Since pollutants are applied at the soil surface, we considered that organic pollutants will be more prone to interact with DOMSURF, which is rich in phenolic compounds. Physical nonequilibrium transport conditions were identified and quantified with PolDOC. Model showed that the Bt horizon acted as a sink to partly retain DOMSURF. While differences in ISO and SMX transport could be explained by different sorption reactivity with the soil solid phase, the increased leaching of EPX in presence of DOMSURF required the activation of co-transport with DOMSURF

Modeling water and isoproturon dynamics in a heterogeneous soil profile under different urban waste compost applications

International audienceCompost amendments and tillage practices can modify soil structure and create heterogeneities at the local scale. Tillage affects soil physical properties and consequently water and solute transport in soil, while compost addition to soil influences pesticide sorption and degradation processes. Based on the long-term field experiment QualiAgro (a INRA–Veolia partnership), a modeling study was carried out using HYDRUS-2D to evaluate how two different compost types combined with the presence of heterogeneities due to tillage affect water and isoproturon dynamics in soil compared to a control plot. A municipal solid waste compost (MSW) and a co-compost of sewage sludge and green wastes (SGW) have been applied to experimental plots. In each plot, wick lysimeters, TDR probes, and tensiometers were installed to monitor water and solute dynamics. In the plowed layer, four zones differing in their structure were identified: compacted clods, non-compacted soil, interfurrows, and the plow pan. From 2004 to 2010, the unamended control (CONT) plot had the largest cumulative water outflow (1388 mm) compared to the MSW plot (962 mm) and SGW plot (979 mm). After calibration, the model was able to describe cumulative water outflow for the whole 2004–2010 period with a model efficiency value of 0.99 for all three plots. The CONT plot had the largest isoproturon cumulated leaching (21.31 μg) while similar cumulated isoproturon leaching was measured in the SGW (0.663 μg) and MSW (0.245 μg) plots. The model was able to simulate isoproturon leaching patterns except for the large preferential flow events that were observed in the MSW and CONT plots. The timing of these preferential flow events could be reproduced by the model but not their magnitude. Modeling results indicate that spatial and temporal variations in pesticide degradation rate due to tillage and compost application play a major role in the dynamics of isoproturon leaching. Both types of compost were found to reduce isoproturon leaching on the 6 year duration of the experiment

Integrating X-ray CT data into models

X-ray Computed Tomography (X-ray CT) offers important 4-D (i.e., 3-D scanning over time) structural information of the soil architecture. This imaging tool provides access to the 3-D morphological properties of the soil pore space such as the 3-D connectivity of pores that are essential to the understanding of water, solute, and gas transport processes. Other morphological properties such as pore-size distribution, specific surface area, or spatial heterogeneity of soil can be obtained from the X-ray CT images. Many studies have used this technique to better understand the evolution of macroscopic soil physical properties such as structural stability and relate it to spatial descriptors of soil pore space morphology when the soil undergoes wetting/drying cycles (e.g., Diel et al., 2019) or when it is subjected to different agricultural practices (e.g., Papadopoulos et al., 2009; Dal Ferro et al., 2013; Caplan et al., 2017). Non-equilibrium transfer processes, such as preferential transport, have also been related to the quantification of macropores in X-ray CT images (e.g., Larsbo et al., 2014; Katuwal et al., 2015; Soto-Gómez et al., 2018). In addition, X-ray CT data have proved particularly useful for reconstructing the skeletons of biopore networks, such as those burrowed by earthworms (Capowiez et al., 1998), and for monitoring their temporal dynamics (Joschko et al., 1993) (see Chap. 10). The role of air-filled soil pores and in particular their connectivity in 3-D in the transport of microbial-generated gaseous products (N2O, CO2) have been hypothesized (Rabot et al., 2015; Porre et al., 2016). X-ray CT data have also provided new knowledge about the 3-D architecture of root systems (e.g., Helliwell et al., 2013) and their impact on the 3-D soil architecture (see Chap. 9). For instance, root hairs were shown to modify the pore-size distribution and connectivity in the rhizosphere (e.g., Keyes et al., 2013; Koebernick et al., 2017, 2019). X-ray CT measurements have also allowed imaging aerenchymatous roots and the gas bubbles entrapped in the soil of rice paddies to explain transport of CO2 and O2 between roots and the atmosphere (Kirk et al., 2019). The dynamics of the spatial dispersion of soil microorganisms could be related to the 3-D description of the pore space obtained by X-ray CT (Juyal et al., 2020). The role of some pore-size classes could also be linked with soil carbon storage (Kravchenko et al., 2020) (see Chap. 10).XP is a María Zambrano Fellow at the Public University of Navarra (UPNA) and acknowledges funding from the European Union - NextGenerationEU through the Spanish program "Ayuda para la Recualificación del Sistema Universitario Español". AE acknowledges funding from Swiss National Science Foundation: Grants P2EZP2 175128 and P400PB_186751. TR was funded by ERC Consolidator grant 646809 DIMR