Over the last decade, the joint development of soil imaging tools and microscale models has made possible to start quantifying the role of soil architecture on soil functions and in particular on soil microbial activity. Microscale heterogeneity of soils have been considered to explain the microbial response, developing the concept of ‘hot-spots'. A major result highlighted from these studies is that spatial accessibility between the trophic resource and soil microorganisms is a key factor (Dungait et al., 2012). Under conditions of limited access, the decomposition of soil organic matter can be drastically reduced, whereas under conditions of optimal access the physiological traits of the microorganisms control the decomposition rate (Vogel et al., 2018). Interactions between soil architecture and microbial dynamics can also be indirect through the degree of soil pore aeration. For instance, the spatial accessibility between particulate organic matter and aerated soil pores can be related to the N₂O production of soil samples (Ortega et al., 2023). New indicators quantifying the spatial accessibility are now emerging (Mbé et al., 2021 ; Rohe et al., 2021). Such spatial indicators of soil heterogeneity could feed the pedotransfer functions used to modulate organic matter decomposition rate in macroscale models of soil carbon dynamics. However the relevance and the robustness of these indicators to explain microbial activity remain to be evaluated (Schlüter et al., 2022). They have been established for static environmental conditions while soil architecture is highly dynamical, continuously changing under biotic and abiotic factors. Due to the complexity of obtaining sequential imaging datasets, few studies have imaged the 3D dynamics of soil architecture (Bottinelli et al., 2016). Mathematical models simulating the deformation of the 3D arrangement of solid particles using geomechanics laws for granular media (Duriez & Galusinski, 2021) or using fractal approaches for simplified soils (Perrier, 1995) have been developed. Other microscale modelling studies have attempted to simulate soil architecture dynamics through the action of microbes or physico-chemical processes using simplified rules (Crawford et al., 2012 ; Rupp et al., 2019). These incentive models have yet to be used to simulate microbial soil functions. We discuss these approaches and how they could be used to investigate to what extent the dynamics of soil architecture modifies the spatial accessibility between organic matter and microorganisms and in fine the soil organic matter decomposition rate.

References:

Bottinelli et al., 2016. Geoderma 65, 78-86.

Crawford et al., 2012. J R Soc Interface 9, 1302-1310.

Dungait et al., 2012. Global Change Biology 18, 1781-1796.

Duriez & Galusinski, 2021. Computers & Geosciences 15, 104936.

Mbé et al., 2021. Eur J Soil Sci., 13144

Ortega et al., 2023. Geoderma, 116224.

Perrier , 1995. PhD Thesis.

Rupp et al., 2019. Front Environ Sci. 7, 170.

Schlüter et al., 2022. Soil, 8, 253–267.

Vogel et al., 2018. Ecological Modelling 383, 10-22.

How to cite: Pot, V., Chenu, C., Garnier, P., and Portell, X.: Towards a quantification of the interactions between soil architecture and microbial dynamics under a dynamical soil architecture, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12922, https://doi.org/10.5194/egusphere-egu23-12922, 2023.

The characteristics of the soil pore network condition the flow of nutrients, liquids, gases, and temperature through this medium. We hypothesized that soil structure properties will also control soil microbial processes. To test this, we selected soil samples where land use generated differences in soil structure. Unaltered soil samples from three adjacent plots were analysed: a potato field soil, ploughed after harvesting, two weeks before sampling (Control); another ploughed potato plot, in which bioaugmentators (plant growth promoting bacteria) had been applied to increase soil biodiversity (Bio); and a third soil, dedicated to melon cultivation, without bioaugmentation, followed by six months of fallow (Melon). In each soil, three different depths were analysed (between 0/-3.33 cm; -3.33/-6.67 cm; and -6.67/-10 cm), and, at each depth, we separated aggregates into three size categories: >0.8 cm, 0.8-0.2 cm, and <0.2 cm. The structure of each core was analysed by computed tomography, while the leucine incorporation method (bacterial growth) and the acetate incorporation into ergosterol method (fungal growth) were used to estimate rates of microbial growth, and respiration was measured to estimate soil decomposer functioning.

The land uses affected soil structural variables. Bio pores had a significantly higher number of branches than Control and Melon. Regarding the aggregate fraction, most of the parameters considered (physical and biological) showed significant differences: the matrix fraction pores (aggregates < 0.2 cm) had a higher connectivity, were more tortuous, but presented a lower number of branches and junctions. On the other hand, there were also lower rates of bacterial growth, fungal growth and respiration in larger aggregates. No significant differences were found considering depth.

We detected links between rates of microbial growth, decomposer functioning and the porous network characteristic differences between samples. The fractal dimension was generally correlated with bacterial growth (r = 0.43, p-value = 0.04), also within Control (r = 0.86, p-value = 0.03) and Melon (r = 0.88, p-value = 0.02) land uses but not for Bio (r = 0.51, p-value = 0.30). Bacterial growth also increased in higher pore tortuosity (r = 0.49, p-value = 0.02), but was inversely correlated with the proportion of pores that end in the matrix (r = -0.41, p-value = 0.05). In the Bio treatment, microbial growth and decomposer were more independent of the pore architecture, and less correlated than in Control and Melon treatments. There, bacterial growth was favoured by higher connectivity (r > 0.86) and optical density (r > 0.69), while respiration increased with the number of pores (r > 0.75) and pore length (r > 0.71). The respiration rate within small aggregates (0.2 to 0.8 cm) increased with the length and number of pores (r > 0.84).

In conclusion, aggregation seems to have a greater effect on the physical and biological properties of the soil than differences between land uses studied and the depths considered. On the other hand, characteristics such as connectivity, tortuosity, and the length and number of pores seem to regulate both bacterial growth and respiration, while fungal growth appears independent.

How to cite: Soto Gómez, D., López Periago, J. E., Fernández Calviño, D., Rousk, J., and Rodríguez Pérez, P.: Bacterial growth and decomposition are regulated by soil pore network characteristics, while fungi are independent: insights from computed tomography, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-2544, https://doi.org/10.5194/egusphere-egu23-2544, 2023.

Nitrous oxide (N₂O) is a greenhouse gas almost 300 times more powerful than CO₂ in terms of global warming potential, and it is also the first ozone-depleting substance emitted in the 21st century. Approximately 43% of N₂O emissions are estimated to be due to anthropogenic activities worldwide, and 52% of this anthropogenic part come from cultivated soils. The main cause of anthropogenic emissions is nitrogen fertilization.

The production, transfer and emission of N₂O from soils are complex multifactorial processes, with a high spatial and temporal variability. Although N₂O production in soils has multiple origins, the main source remains denitrification reactions during microbial respiration under anaerobic conditions. Thus, one of the major soil control factors is the availability of oxygen to soil organisms, which partly depends on the soil structure. The spatiotemporal variability of N₂O emissions is explored by deterministic studies that focus either on the soil microstructure scale, i.e. the scale of N₂O production and microorganism habitat, or on the macrostructure scale, to focus on fluids transfers. However, the influence of soil micro- and macrostructure studied together on N₂O emissions is still poorly known, and represents the objective of this work.

A multi-scale approach was adopted to better understand the determinism of N₂O emissions. The spatial variability of N₂O emissions at the field scale was estimated during a snap-shot campaign on the same soil type with contrasted structural states, induced by different agricultural practices (4 soil modalities crossing strip-till and tillage with compacted or uncompacted areas). 24 soil cylinders were collected in low and high N₂O emission zones and were then scanned by using both X-ray macro- and micro-tomography. Quantitative morphological tools were used to describe soil structure at the macro and micro scales while simultaneously studying other soil properties influencing N₂O emissions (air permeability, gas diffusivity, nitrogen, pH, soil texture, etc.). The 4 soil modalities studied showed contrasted N₂O emissions along with contrasting macrostructural and gas transfer indices. The ongoing work is aimed at clarifying the relationships between multiscale soil structure, gas transfer and other soil factors on N₂O emissions.

How to cite: Maillet, E., Cousin, I., Lacoste, M., and Grossel, A.: Soil N2O emissions: how much does soil structure matter?, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-15651, https://doi.org/10.5194/egusphere-egu23-15651, 2023.

Calcareous soils are common in arid and semi-arid regions and account for around half of the earth surface. In addition to the more widely studied soil organic carbon (SOC) pools, these soils also hold a large stock of soil inorganic carbon (SIC) surpassing SOC stocks. Nonetheless, despite their relevance, the effect of the interplay between SOC and SIC in calcareous soils is still poorly understood.

Soil carbonates can dissolve and re-precipitate in soil pores in short periods of time, dynamically changing the soil pore space, causing direct and indirect impacts on the SOC cycle that increase organic matter turnover rates (Fernández-Ugalde et al., 2011) than in soils of similar characteristics (climate, clay content, etc) without carbonates. This can be partially caused by the fact that carbonates dynamics (dissolution-precipitation) contributes somehow to a slower mineralization of organic matter. Several hypotheses exist to explain this positive effect for the stabilisation of SOC. One is the abundance of Ca that would favour mineral-mineral and organo-mineral interactions and associations. Another is that carbonates can protect SOC from further degradation by cementation. This can be related to carbonate crystals interfering with SOC mineralization by microorganisms.

We use a combination of 3D X-ray Computed Tomography and new mechanistic modelling to determine the relationship between the presence of carbonates in soil (and their dynamics) on the SOC mineralization rates (modelled). Preliminary results will be presented in this contribution.

Soil samples subject to different treatments were obtained from two soil sites: Arazuri (Navarra, Spain) and Rodezno (Rioja, Spain). The Arazuri soil supports a long-term experiment assessing the effect of the continuous application of sewage sludge on agricultural soil quality and productivity. Two contrasting fertilisation treatments corresponding to a baseline (mineral fertilization) and a high organic fertilisation treatment (80 t ha^-1 of sewage sludge) were selected. Rodezno samples were obtained in an agricultural field subject to identical historical agricultural management for decades but naturally presenting two types of soils, differing in their carbonate content in their upper horizon (none and 20% equivalent calcium carbonate) due to their position on the landscape. Air-dried soil aggregates were scanned using a Nikon XT H 225ST X-ray CT system at two voxel resolutions 5 µm (2-5 mm aggregate size) and 25 µm (> 5 mm aggregate size). In parallel, a spatially-explicit mechanistic model of the SOC dynamics (Portell et al. 2018) considering explicitly the role of soil bacteria was expanded to take into account the modifications of the soil architecture due to the presence of soil carbonates as observed in the scanned samples.

Image-analysis of the X-ray CT data allowed to quantify the effect of calcium and organic fertilisation in the pore space distribution and connectivity. In addition, the combination of imaging data and the mechanistic model allowed to estimate mineralisation rates and link them to the calcium carbonate content and fertilisation treatment. Overall, our research provides a deeper understanding of the soil carbon organic and inorganic cycles.

References: Fernández-Ugalde et al. (2011). Geoderma,164: 203-214; Portell et al. (2018) Front. Microbiol. 9:1583.

How to cite: Portell, X., de Soto, I. S., Otten, W., Hallett, P. D., and Virto, I.: Mechanistic understanding of the effect of soil carbonates and organic amendments on soil structure and biological activity., EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13683, https://doi.org/10.5194/egusphere-egu23-13683, 2023.

The advancements of agriculture practices and technologies in harnessing natural resources has been a major component of humanity's development to produce and maintain food safety. As the bed for agricultural crops, soils are a major natural resource, and soil structure plays a crucial role in agricultural productivity. Long term differences in land use and agronomic management result in differences in soil physical structure, which also translates into variations in pore networks. Decomposition of organic matter and, hence, soil carbon storage capacity are closely related to the pore domain, which is the main environment where chemical and biological processes leading to carbon protection or decomposition take place. In this study, we explored pore structure, carbon characteristics, and their relationships in contrasting ecological systems from a long-term (> 30 years) experiment located at Kellogg Biological Station (Michigan, USA). The studied systems are (i) an agricultural intensively managed system of corn-soybean-wheat rotation (CT), (ii) a native early successional community abandoned from agriculture in 1989 (ES), (iii) a mowed grassland that has never been tilled or in agriculture (NTG), and (iv) late-successional deciduous forest that has never been cleared for agriculture (DF). An x-ray tomography analysis of intact soil cores was used to investigate pore size distributions, connectivity, and morphology to assess soil pore structure. We also measured total soil carbon and nitrogen contents, mineral associated organic carbon (MAOM), and particulate organic carbon (POM), short- and long-term soil respiration, and microbial biomass carbon. Preliminary results showed that the volumes of the soil pores with 30-180 mm Ø, the size range considered as the optimal microbial habitat, followed the trend of DF>NTG »ES>CT. The nitrogen and carbon content of these systems are also in agreement with this trend. Interestingly, MAOM fraction, considered to be a more recalcitrant form of carbon, followed the same trend, while the ratio of MAOM to total organic carbon did not change notably among the systems.

How to cite: Dor, M., Fan, L., Zamanian, K., and Kravchenko, A.: Long-term contrasting land uses influence on soil pore structure and organic carbon, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-10771, https://doi.org/10.5194/egusphere-egu23-10771, 2023.

Field scale is a key scale for soil quality management in cropland, particularly for organic carbon and nutrient contents. To cope with within field variability, composite samples are collected which allows determining inexpensive average analytical properties for purposes such as soil quality monitoring. This is not feasible for most soil physical properties which require the collection of undisturbed soil samples for their determination. Unfortunately, most physical properties show large and unpredictable variability, thus leading to heavy soil sampling, laboratory costs and physical data processing to determine field properties and their time trend. Shrinkage analysis (ShA) provides a characterization of the soil pores, their air and water equilibrium and the soil structure stability, on the full soil water content range. It is usually performed on undisturbed soil samples; however, it was also performed on repacked soil samples from 2 mm size hand-fractioned aggregates. Moreover, it characterizes the physical properties of the two pore systems, namely the structural pores and the plasma pores. The later can be assumed to remain unchanged upon fractionation. Oppositely, the coarser structural pores are obviously destroyed. However, the intra aggregate structure and, therefore, the smaller size structural pores, might be conserved. In the frame of a large scale on-farm diagnosis of soil quality, we hypothesized that a part of the soil physical properties quantified with ShA could be characterized on repacked composite soil samples collected at field scale. This was tested by comparing (i) the physical properties of undisturbed soil samples and repacked soil samples on a wide range of soil types and quality and (ii) the relationships between soil organic carbon content, soil clay content, and the physical properties of undisturbed and repacked soil samples, respectively. 

How to cite: Deluz, C., Boivin, P., Keller, T., and Dötterl, S.: Compared physical properties of repacked and undisturbed soil samples as assessed by shrinkage analysis: method, interest and limitations, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16637, https://doi.org/10.5194/egusphere-egu23-16637, 2023.

Animal behavior is a complex trait known to have strong feedbacks with environmental conditions across all ecosystems. Understanding how animals interact with their environment is therefore a key element for gaining new insights on how ecosystem landscapes develop and what is the potential environmental degradation caused by different species of animals. Within animal behavioral traits, characterizing animal movement has received attention because it is relatively easy to monitor. Despite the widely differing conditions in which different species of animals exist, it has been demonstrated that statistical models of animal movement based on random walks (e.g., Brownian and Lévy walks) often offer a consistent and accurate representation of animal movement in diverse ecosystems. Grazing livestock systems are particularly interesting to explore as they play an important role in the context of climate change and agricultural sustainability. Movement of grazing livestock has not been fully explored nor described, and knowledge on the way they impact the environment temporally and spatially is often empirical and remains largely unknown. To fill these gaps and to provide new insights on spatio-temporal impacts of grazing animals on soil structure, we characterized daily and seasonal patterns of grazing livestock using GPS (Global Positioning System) data from conventionally grazed and cell-grazed paddocks. In addition, we used a soil compaction model to predict changes in bulk density due to grazing. We found that the way grazing livestock move is consistent with a Lévy walk and that Lévy properties depend on the dimensions of the grazing cells (constraints and attractors). The combination of an animal movement model and a soil compaction model allowed us to obtain treatment-specific spatially explicit maps of soil properties affected by grazing that are consistent with observations.

How to cite: Romero-Ruiz, A., De-Meo-Filho, P., Pulley, S., Segura, C., Rivero-Viera, J., Coleman, K., Cardenas, L., Milne, A., and Whitmore, A. P.: Grazing livestock move by Lévy walks: Implications for soil structure dynamics, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9069, https://doi.org/10.5194/egusphere-egu23-9069, 2023.

Deep burrowing earthworms produce exudates that coat the biopore wall with compacted finer-textured and organic matter-rich. The coating exhibit high spatial heterogeneity that, although connected to the inter- and intra-aggregate pore network in structured soils, can limit the flow exchange between the macropore and the soil matrix during preferential flow. Such flow exchange can be dynamically quantified if known the complex hydro-mechanical interrelations between biopore structure and soil matrix affecting the stress-strain behaviour at macroscopic scale. Our hypothesis was that the hydro-mechanical interrelations may be described with the discrete element method (DEM) coupled with the pore finite volume (PFV) approach if the model reproduces the pore network between coating and soil aggregates. Therefore, the objective was to develop a coupled DEM-PFV model together with a parameterization procedure based on machine learning algorithm to find the dependency between macroscopic mechanical and hydraulic soil properties obtained from drainage experiments of biopore samples to calibrate micro parameters of the model. The solid phase of the soil matrix was created using DEM inside a cube of about 5 cm edge, randomly filled with two aggregate sizes of 1 mm diameter (constituted by particles of 0.052 mm in diameter) and 0.4 mm diameter (constituted by particles of 0.03 mm in diameter). The pack of aggregates was compressed until the porosity reached the experimental value. The coating surface was created with a thickness of 0.25 mm and particles of 0.015 mm in diameter and compressed to reproduce the experimental porosity. The DEM models were coupled with a two-phase PFV model (2PFV) to simulate hydro mechanical effects during drainage. A total of 500 drainage simulations were performed for matrix and coated sample by randomly varying particle Young's modulus and bond strength. Saturation and strain along with the pressure head were measured to train the machine learning algorithm. The drainage experiments were designed to promote the movement of water from the soil matrix across the coated burrow surface. Thus, the samples were placed in the sandbox with the coated burrow in contact with the sand layer. An optical-laser sensor together with a tensiometer were used to quantify the pressure-head and sample shrinkage while the pressure was reduced at a rate of approximately 50 Pa s^-1. In total, 40 samples of each treatment were used in these measurements. The poly-dispersed DEM-2PFV model was able to reproduce the pore network of coating material and the inter- and intra-aggregate pore network of the matrix that changed dynamically with the increment of pressure head. The machine learning model revealed that the bond strength among particles within aggregates governed the shrinkage of soil matrix, while the particle stiffness of the coating material reduced the susceptibility of aggregate breakage producing a more stable inter-aggregated pore network during the drainage process. This study confirmed that coating material present in biopore surface increases the horizontal soil hydro structural stability. The microscale hydro-mechanic modelling can be useful for finding flow exchange parameters inputs for upscaled models and correlating pore-scale parameters to experimentally determined stress-strain macro parameters.

How to cite: Barbosa, L. A. and Gerke, H. H.: A discrete element model for describing coupled hydro-mechanical processes during drying of soils with coated worm burrows, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16408, https://doi.org/10.5194/egusphere-egu23-16408, 2023.

Despite the large contribution of macropores made by soil engineers to the soil macroporosity and water infiltration, few studies have addressed the specific contribution of soil engineer groups, dynamics of biopores and their efficiency in conducting water. Thus, we aimed to investigate the link between soil macrofauna, soil biopores and water infiltration under different pedoclimatic conditions. To do so, we conducted an experimentation in twelve study sites with a large longitudinal gradient from France to Vietnam.  The experiment consisted in the field incubation of repacked soil in cores (15 cm in height and 15 cm in diameter) and controlling the activity of soil engineers in the manner of litter bag. For each site, soil columns were: (i) covered with a mesh (200µm) or not and (ii) with or without addition of organic residues to the soil surface. After 12 months, we measured (i) the 3D organization of biopores by X-ray computed tomography and (ii) the saturated hydraulic conductivity by Beerkan method. In addition, soil macrofauna communities and the 3D organization of biopores was measured in each study field. 

Addition of organic residues increased up to 2-fold the volume percentage of biopores which reached similar values than those observed for each study field. The co-inertia analysis between the data matrix characterizing the shape of biopores and the data matrix of the macrofauna communities showed no statistically significant correlation. Saturated hydraulic conductivity increased with the presence of biopores by 2 to 50-fold with the lowest increased in soils presenting largest saturated hydraulic conductivity. In conclusion, these results demonstrated that biopores are rapidly regenerated regardless the pedoclimatic conditions while the efficiency of biopores in conducting water is related to soil properties.

How to cite: Védère, C., Aroui Boukbida, H., Capowiez, Y., Cheik, S., Coulouma, G., Pham Dinh, R., Grellier, S., Hammecker, C., Henry des Tureaux, T., Harit, A., Janeau, J.-L., Jouquet, P., Maeght, J.-L., Rumpel, C., Sammartino, S., Silvera, N., Siltecho, S., Smaili, L., Soulileuth, B., and Bottinelli, N.: Diversity of soil biopores and their influence on soil water infiltration under various pedoclimatic conditions, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-3366, https://doi.org/10.5194/egusphere-egu23-3366, 2023.