SSS6.1 | Soil structure, its dynamics and its relevance to soil functions: feedbacks with soil biology and impacts of climatic conditions and soil management
Soil structure, its dynamics and its relevance to soil functions: feedbacks with soil biology and impacts of climatic conditions and soil management
Convener: Frederic LeutherECSECS | Co-conveners: Loes van Schaik, John Koestel, Ophélie SauzetECSECS, Ulrich Weller
| Thu, 27 Apr, 10:45–12:30 (CEST)
Room K2
Posters on site
| Attendance Thu, 27 Apr, 08:30–10:15 (CEST)
Hall X3
Posters virtual
| Attendance Thu, 27 Apr, 08:30–10:15 (CEST)
vHall SSS
Orals |
Thu, 10:45
Thu, 08:30
Thu, 08:30
Soil structure and its stability determine soil physical functions and chemical properties such as water retention, hydraulic conductivity, susceptibility to erosion, and redox potentials. These soil physical and chemical characteristics are fundamental for biological processes, among them root penetration and organic matter and nutrient dynamics. The soil pore network forms the habitat for soil biota, which in turn actively reshape it, often favorable to their needs. The soil biota, root growth, land management practices like tillage and abiotic drivers (e.g. wetting/drying cycles) lead to a constant evolution of the arrangement of pores, minerals and organic matter. With this, also the soil functions and properties are perpetually changing. The importance of the interaction between soil structure (and thus soil functions) on one side and soil biology, climate and soil management on the other, is highlighted by recent research outcomes, which are based on advanced imaging techniques, novel experimental setups and modelling approaches. Still, present studies have barely scratched the surface of what there is to discover.
In this session, we are inviting contributions on the formation and alteration of soil structure and its associated soil functions over time. Special focuses are on feedbacks between soil structure dynamics and soil biology as well as the impact of mechanical stress exerted by heavy vehicles deployed under land management operations. Further, we encourage submissions that are exploring new modelling concepts, integrating complementary measurement techniques or aim at bridging different scales.

Orals: Thu, 27 Apr | Room K2

Chairpersons: Loes van Schaik, John Koestel, Ophélie Sauzet
On-site presentation
Valérie Pot, Claire Chenu, Patricia Garnier, and Xavier Portell

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.



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,, 2023.

On-site presentation
Diego Soto Gómez, José Eugenio López Periago, David Fernández Calviño, Johannes Rousk, and Paula Rodríguez Pérez

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,, 2023.

On-site presentation
Emile Maillet, Isabelle Cousin, Marine Lacoste, and Agnes Grossel

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,, 2023.

On-site presentation
Xavier Portell, Isabel S. de Soto, Wilfred Otten, Paul D. Hallett, and Iñigo Virto

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,, 2023.

Virtual presentation
Maoz Dor, Lichao Fan, Kazem Zamanian, and Alexandra Kravchenko

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,, 2023.

On-site presentation
Cédric Deluz, Pascal Boivin, Thomas Keller, and Sebastian Dötterl

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,, 2023.

On-site presentation
Alejandro Romero-Ruiz, Paulo De-Meo-Filho, Simon Pulley, Carmen Segura, Jordana Rivero-Viera, Kevin Coleman, Laura Cardenas, Alice Milne, and Andy P. Whitmore

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,, 2023.

Virtual presentation
Luis Alfredo Barbosa and Horst H. Gerke

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,, 2023.

On-site presentation
Charlotte Védère, Hanane Aroui Boukbida, Yvan Capowiez, Sougueh Cheik, Guillaume Coulouma, Rinh Pham Dinh, Séraphine Grellier, Claude Hammecker, Thierry Henry des Tureaux, Ajay Harit, Jean-Louis Janeau, Pascal Jouquet, Jean-Luc Maeght, Cornelia Rumpel, Stéphane Sammartino, Norbert Silvera, Siwaporn Siltecho, Lotfi Smaili, Bounsamay Soulileuth, and Nicolas Bottinelli

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,, 2023.

Posters on site: Thu, 27 Apr, 08:30–10:15 | Hall X3

Chairpersons: Frederic Leuther, Ulrich Weller
Determining Soil Microbial Activity Based on Soil Moisture and Average Functions
Yulissa Perez Rojas and Teamrat Ghezzehei
Zhao Zheng and Pan Genxing

Heterogeneous soil-landscapes with varying land uses and land covers are common in the hilly areas of the lower Yangtze valley of China. Variations of soil quality, mainly driven by soil organic matter and soil aggregation, across these soil-landscapes impacts the development of agro-industries in rural areas. How the development of macroaggregates (MAC) and their pore structure in relation to soil organic matter and microbial community varies with soil-landscapes (disturbed and undisturbed) remained unclear. Both bulk samples and undisturbed cores were collected from topsoil (0-15 cm) respectively on forestland (FL) under vegetation conservation on the hill slope, orchard (OR) and upland cropland (UL) on the slope and paddy fields (PF) in the basin in a small watershed from suburb Nanjing of China. Soil organic carbon (SOC) pools and microbial phospholipid fatty acids (PLFAs) as well as basic physico-chemical properties were measured while size fractionation of water-stable aggregates were performed. Further, the pore structure of the macroaggregate samples were analyzed with X-ray micro-computed tomography (X-ray μCT). Compared to FL, topsoil SOC was lower by 54%-70%, soil aggregate stability by 41-67% and total PLFAs by 14%-42% under the disturbed agricultural soil-landscapes. The mass fraction of macroaggregates was lower in OR, UL and PF, by over 44%. The total porosity of the macroaggregates, estimated by the μCT images, was lower by 17% and 33% under UL and OR though unchanged under PF. A similar trend was found for the connected porosity and total throat area. To note, both SOC and microbial PLFAs of the macroaggregate samples were significantly positively correlated to total porosity, connected porosity and total throat area, across the landscapes. Overall, soil quality was seen profoundly reduced in the disturbed soil-landscapes under agricultural activities although PF was shown most close to FL in the context of organic carbon stabilization and microbial biomass conservation. Thus, improving rice paddy management through soil organic matter conservation and macroaggregation could contribute to sustaining local soil quality for better agricultural development in the hilly rural area.

How to cite: Zheng, Z. and Genxing, P.: Changes in microbial community and soil organic matter mediated by macroaggregate pore structure across soil-landscapes in a hilly watershed, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-6755,, 2023.

Martina Sobotkova, Alexandr Zak, Michal Snehota, and Michal Benes

Freezing and thawing cycles in laboratory were studied. Freezing-thawing cycles were carried out in the laboratory on fully saturated packed sand sample (15 cm in diameter and 20 cm in height). Series of freezing-thawing cycles were conducted with newly designed experimental setup. The setup consisted of inner plastic tube covered on its sides and outer plastic tube. The column sample was placed into the precisely controlled freezer chamber. The top of the sample was covered by an aluminum lid. Initially the sample was equilibrated at +10 °C then the temperature inside the chamber was changed to -10 °C. The inner temperature of the sample was monitored in three depths by thin temperature sensors (109 SS, Campbell Scientific, USA) horizontally inserted into the sample. The experiment aims to provide information on freezing dynamics and thermo-mechanical changes during the freezing and thawing cycles. Horizontal gradient within freezing cycle was monitored. The data were compared with simulations obtained by a numerical model (Žák et al., 2013). The model is based on the heat balance within the sample assembly and a modified heat equation for the porous medium temperature allowing for the phase transition below the freezing point depression. 

How to cite: Sobotkova, M., Zak, A., Snehota, M., and Benes, M.: Freezing-Thawing Cycles of Saturated Sand Sample, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13930,, 2023.

Tobias Klöffel, Mats Larsbo, Nicholas Jarvis, and Jennie Barron

Freeze-thaw (FT) cycles have shown to affect the evolution of the pore space of agricultural soils, thereby affecting their hydraulic properties. In the temperate-boreal zones, FT patterns are projected to shift from relatively long and uniform freezing periods to more frequent fluctuations around 0°C as a result of climate change. To better anticipate potential consequences for water storage and flows in agricultural soils, a thorough evaluation of the importance of FT cycles in this context is required.

Here we summarize the findings of studies investigating the effects of FT cycles on various pore-space characteristics (e.g. macroporosity, pore connectivity, percolating pore space) and hydraulic properties (e.g. infiltration capacity, hydraulic conductivity, water retention) of agricultural soils. This includes the results of a laboratory experiment where we simulated different FT scenarios representative for current and future winter conditions in the temperate-boreal zones.

Our findings suggest that a shift in FT patterns with climate change indeed has the potential to alter, at least temporarily, water retention properties and (near-)saturated hydraulic conductivities of agricultural soils. We highlight that this is despite most changes in pore-space characteristics seem to occur in pores with a diameter smaller than 50 µm. The persisting increase in pore connectivity of specific soils with an increasing number of FT cycles appears to be decisive in this respect. However, to assess fully the magnitude of changes in soil water functions at the field scale may require modelling. We finally stress that the sensitivity of hydraulic properties to FT patterns questions the transferability of results of some previous studies to the natural environment, applying unrealistic temperatures and rates of freezing and thawing.

How to cite: Klöffel, T., Larsbo, M., Jarvis, N., and Barron, J.: Freeze-thaw effects on pore space and hydraulic properties of agricultural soils – a summary of studies and implications for the temperate-boreal zones in a changing climate, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-6054,, 2023.

Michal Snehota, Martina Sobotkova, Tomas Princ, Jan Sklenar, Martin Jex, Michal Benes, and Andreas J Pohlmeier

In this study, magnetic resonance imaging (MRI) was used to investigate the freezing and thawing process of a series of repacked samples of sand, soil, and sand-soil mixture. The samples were placed in a thermally insulated container inside a vertical bore MRI scanner and cooled by flowing cold gaseous nitrogen through a porous material at the top of the container. Temperatures were monitored in several points above the sample and at the sample surface, and a marker placed on the sample surface was used to measure sample deformation. A 4.7 T magnet was used for MRI and the Multiple-Slice Spin-Echo (MSME) and Zero Echo Time (ZTE) pulse sequences were employed to obtain the images. The contrast between the frozen and unfrozen water in the samples was given by the substantial difference in T1 and T2 relaxation times between the two states. The hydrogen in the frozen water does not produce any signal for both pulse sequences, thus all the signal represent the liquid/unfrozen water. The time-lapse three-dimensional (3D) imaging was performed during the entire course of the experiment with alternating use of the MSME and ZTE imaging techniques. Once the freezing front reached near the bottom of the sample, the thawing process was initiated by switching the inflow of cooling gas to the inflow of nitrogen at room temperature. The small changes in sand structure as a consequence of volumetric ice-water changes were studied using spatiotemporal analysis of the freezing front advancement and frozen water volume. The study detected interesting patterns of preferential thawing on the onset of thawing process in the case of sand. The MSME pulse sequence was successfully used to image the process in the sand, whereas the ZTE was capable of detecting water in the finer soil material. The data obtained in the study were used to develop two-phase ice-water simulation models to interpret the experimental results and better understand the freezing and thawing phenomena.

How to cite: Snehota, M., Sobotkova, M., Princ, T., Sklenar, J., Jex, M., Benes, M., and Pohlmeier, A. J.: Integrating MRI and modeling for Understanding Freeze-Thaw Processes in Saturated Soil and Sand, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12345,, 2023.

Mats Larsbo, Johannes Koestel, Eveline Krab, and Jonatan Klaminder

The rate at which soil becomes physically mixed due to earthworm actions (bioturbation) has relevance for the fate of nutrients and pollutants and for the soil’s ability to sequester carbon. Nevertheless, methods to quantify bioturbation under field-like conditions are largely lacking. The soils of the Fennoscandian tundra offer a special possibility to quantify bioturbation, because they have developed in the absence of soil burrowing macrofauna. They commonly exhibit a thick organic layer on top of the mineral soil with a sharp layer boundary. The bulk density of the two soil layers differs markedly. Since bioturbation mixes both soil layers, the temporal changes in the bulk density profile of such soils may be exploited to estimate bioturbation rates in the field. In this study, we applied a model for earthworm bioturbation to observed changes in soil densities occurring in a mesocosm experiment with intact soil carried out in the arctic during four summers. We show that changes in soil density profiles can indeed be used to infer realistic earthworm bioturbation rates. Although uncertainties in parameter values were sometimes large, the results from this study suggest that soil turnover rates and endogeic earthworm soil ingestion rates in tundra soils may be as high as those reported for temperate conditions. Such large bioturbation rates can explain observed large morphological changes in nearby soils where dispersing earthworms have resulted in complete inmixing of the organic layer into the mineral soil. Our model is applicable to soil profiles with marked vertical differences in bulk density such as the soils of the Fennoscandian tundra where earthworms are currently dispersing into new areas and to layered repacked soil samples that are incubated in the field.

How to cite: Larsbo, M., Koestel, J., Krab, E., and Klaminder, J.: Quantifying earthworm bioturbation from changes in vertical bulk density profiles, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12630,, 2023.

Petra Heckova, Michal Snehota, John Koestel, Ales Klement, and Radka Kodesova

Constructed soils play an important role in urban hydrology e.g. in the functioning of green roofs and stormwater bioretention cells. Water infiltration, colloid transport, and heat transport are affected by changes in pore system geometry particularly due to the development of macropores and clogging by particles. The aim is to elucidate changes in bioretention cell performance by studying the structural changes of soils at the microscale by invasive and noninvasive methods. Noninvasive visualization methods such as computed microtomography (CT), are an effective mean of soil structure assessment. X-ray CT is capable to investigate soil in terms of structure development, pore-clogging and pore geometry deformations.

Two identical bioretention cells were established in December 2017. The first bioretention cell (BC1) collects the stormwater from the roof of the nearby experimental building (roof area 38 m2). The second bioretention cell BC2 is supplied from a tank using a controlled pump system for simulating artificial rainfall. Each BC is 2.4 m wide and 4.0 m long. The 30 cm thick biofilter soil mixture is composed of 50% sand, 30% compost, and 20% topsoil. Bioretention cells are isolated from the surrounding soil by a waterproof membrane. The regular soil sampling program was initiated in 2018 in order to visualize and quantify the soil structure and internal pore geometry of samples. Undistributed samples were collected from the surface of the filter layer twice a year from each BC. The aluminum sampling cylinders had an internal diameter and height of 29 mm. Three batches of samples were taken during three years. The first set of 24 undisturbed samples was collected upon planting in June 2018, while the second set of 24 samples was taken after the end of the first vegetation period in November 2018. The second batch of 48 samples, were taken in the same period as in the previous year.  The last batch of 24 samples was taken in June 2020. Those collected samples were scanned by CT imaging.

Analyses of pore network morphologies were performed on the scanned samples. Macroporosity, pore thickness, pore connection probability, critical diameter and Euler-Poincare density were determined to understand pore space in the biofilter. Macroporosity in BC1 shows a decreasing trend in the first three periods, it can be a result of soil consolidation. In subsequent periods, macroporosity remains constant in BC1. The characteristic pore connection probability in BC1 also shows a decreasing trend in the first three periods, but compared to the macroporosity, the connectivity increases in the last two periods in BC1. This may be due to plants growth, which was most pronounced in 2019. The samples' most frequently represented pore thickness ranges from 80 to 330 µm in all periods in both BCs. The percentage of these pores was higher than 50% in both BCs.

How to cite: Heckova, P., Snehota, M., Koestel, J., Klement, A., and Kodesova, R.: Soil structure changes of constructed soil in bioretention cell during three years, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-11624,, 2023.

Jari Hyväluoma, Petri Niemi, Kofi Brobbey, Sami Kinnunen, Arttu Miettinen, Riikka Keskinen, and Helena Soinne

Soil management is known to have significant effects on soil structure. Especially, grassland renovation and associated ploughing may have destructive influence on structure, but on the other hand conversion of arable land to grassland can improve pore structure and soil functions. In crop rotations including perennial grasses, soil structure is affected by these counteracting processes. The purpose of this work was to study and quantify the impacts of varying soil management practices on the structure of boreal arable heavy clay soils. We studied intact topsoil samples collected from two sites by X-ray computed microtomography, image analysis, image-based pore-scale flow simulations, and water retention measurements. At both sites, one area under long-term (at least 30-year-old) grassland was compared with adjacent field area with contrasting managements:

  • Site 1: Cereal production under no-till management for 13 years prior to sampling.
  • Site 2: Crop rotation of a livestock farm with cereals and perennial grasses, tillage by ploughing. At the sampling time this field area had been two years under grass after preceding 3-year cereal period.

Both imaging and water retention showed statistically and practically significant differences in the soil macropore structure at site 1 such that porosity of the long-term grassland was clearly higher that that under cereal production. On the contrary, at site 2, only minor differences between managements were observed. Our results show that the soil management practices affect the macropore structure of boreal arable clay soil and that no-till and crop-rotation managements had clearly different effects on soil structure as compared to long-term grasslands.

How to cite: Hyväluoma, J., Niemi, P., Brobbey, K., Kinnunen, S., Miettinen, A., Keskinen, R., and Soinne, H.: Impacts of soil management on the pore structure of boreal arable clay soils, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-11103,, 2023.

Giulia Frutaz, Claudia Meisina, Massimiliano Bordoni, and Rinaldo Sorgenti

Nowadays, changing climate is continuously posing new challenges to land management and conservation, also in built areas and agricultural fields. Polymers such as polyacrylamide (PAM) offer a suitable tool to stem soil degradation, as well as having a wide range of applications. We performed a detailed investigation about this polymer applications with particular attention to the field of slope instabilities through a systematic literature review to assess the extent and the specifics of the research done on Polyacrylamide as an improver of soil features, browsing between more than 800 articles published from 1990 to 2022. Research on polyacrylamide application increased since the 2000s, its main use being the prevention of irrigation-connected erosion, even if in more recent years its ability as a soil stabilizer became more and more newsworthy. We then proceeded to reconstruct soil samples in laboratory to observe the effects of application of anionic polyacrylamide (PAM) on their physical, volumetric, mechanical, and hydrological properties. First, two sets of samples were reconstructed using kaolin and sandy loam soil, respectively, with three different dry densities (varying between 1.2 and 1.6 g/cm3), three different initial water contents (varying between 10% and 40%) and five different polymer application rates (0%, 0.003%, 0.03%, 0.3%, and 1%by weight). The polymer, a granular anionic polyacrylamide, provided by Micronizzazione Innovativa Srl, has been manually applied and mixed with the samples, constituted by pvc cylinders with a diameter of 9.5 cm and 15 cm high. Preliminary results showed that the increase of PAM percentage in samples generally coincided with increase of liquid limit and plasticity index, causing at the same time a more gradual and regular release of samples water compared to untreated samples. These preliminary results can stress on the possible application of PAM to improve other soil features which could impact on slope instabilities occurrence, in a frame of sustainable solutions for reduction of landslides susceptibility, hazard and risk.







Soil conservation

Land degradation

How to cite: Frutaz, G., Meisina, C., Bordoni, M., and Sorgenti, R.: Use of Anionic Polyacrylamide to improve soil properties and challenge slope instabilities: preliminary data, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12086,, 2023.

Effects of steering of tracked combine harvester on shear damage of paddy field soil
Zhao Ding, Ping Xin, and Zhan Su
Clémence Pirlot, Anne-Catherine Renard, and Aurore Degré

Alternative agricultural practices emerge to provide more sustainable productions systems and to meet
tomorrow's diets. These practices and varying climatic conditions will have impacts on soil structure and
thus, on soil hydraulic properties. However, most models do not consider the temporal variability of soil
hydraulic properties, which can lead to poor decision making. Thus, quantifying the temporal evolution of
hydraulic properties is essential to better understand the impact of emerging agricultural practices on soil
structure (Chandrasekhar et al., 2018).

In most studies, temporal variation of soil hydraulic properties is investigated using punctual
measurements in the field or in the laboratory (Alskaf et al., 2021; Geris et al., 2021). Results are often
inconsistent between studies due to the timing and type of measurement performed (Chandrasekhar et
al., 2018; Strudley et al., 2008). In addition, most research focuses on the topsoil layers and does not
consider the longer term effects on the deeper layers of the soil (Wahren et al., 2009).

In this research, temporal evolution of the hydraulic properties of three innovative production systems is
continuously monitored up to 90 cm depth. The three systems are designed to disrupt current agronomic
trials and aim to produce the ingredients of tomorrow’s diets. They are pesticide-free and have long-term
rotations of 8 years with intercrops. These systems are implemented on 8 parcels of the University of
Gembloux Agro-Bio Tech on a typical loamy soil in Belgium.

The innovative systems were instrumented with 24 Teros 12 water content and 24 Teros 21 water
potential sensors from MeterGroup. Both types of sensor are robust and highly accurate. The Teros 12
probes also measure soil temperature and salinity. Potential probes can measure potential over a wide
range of values from -9 to -2000 kPa. All probes are connected to MeterGroup's ZL6 data loggers which
allow real-time data collection. The water content and potential probes are placed in parallel in the first
three soil layers at 30, 60 and 90 cm depth in 8 plots. Intact soil cores are also taken every two months to
determine bulk density and total soil porosity.

The simultaneous determination of both water content and water potential over time under natural
conditions allows the temporal evolution of the hydrodynamic properties to be captured at the level of
the first three horizons. This monitoring will make it possible to quantify the temporal evolution of the
structure of a loamy soil under the effect of alternative agricultural practices and varying climate
conditions. The first two years were contrasted in climatic conditions with a wet and a dry year. In addition,
a diverse range of agricultural practices with different crops such as beet, camelina, corn, rapeseed and
winter wheat were grown in both years. The results of these first two years of monitoring will be presented
at the EGU 2023 General Assembly and compared to theoretical properties that would be obtained using
classical PTF.

How to cite: Pirlot, C., Renard, A.-C., and Degré, A.: Monitoring the temporal evolution of soil structure of three innovative production systems in the field, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-5679,, 2023.

Sara König, Ulrich Weller, Bibiana Betancur-Corredor, Andrey Zaytsev, Ute Wollschläger, and Hans-Jörg Vogel

BODIUM is a systemic soil model that integrates the most important processes and components in soil and at the soil-plant interface in order to predict land management impact on soil functions.

A central role plays soil structure dynamics. Different land use and tillage regimes alter the pore space in a characteristic way. Biological processes such as root growth and earthworm activity contribute to the changes in soil pore structure.

We show model scenarios where different structure dynamics are evaluated in their effect on plant growth, water percolation including fast breakthrough due to macropore flow, and nutrient efficiency.

Parts of the soil structure modeling are supported by the open access soil structure library (; Weller et al., 2022), where characteristic macro- and mesopore architectures obtained from Xray-CT imaging are available for different soil types and soil managements.

The model also allows exploration of climate change scenarios and evaluation of mitigation strategies.


Weller, U., Albrecht, L., Schlüter, S., and Vogel, H.-J.: An open Soil Structure Library based on X-ray CT data, SOIL, 8, 507–515,, 2022.

How to cite: König, S., Weller, U., Betancur-Corredor, B., Zaytsev, A., Wollschläger, U., and Vogel, H.-J.: Soil structure dynamics matters: Modelling the impact of land management on soil functions using BODIUM, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-5106,, 2023.

Nicholas Jarvis, Elsa Coucheney, Mats Larsbo, Elisabet Lewan, and Katharina Meurer

Soil-crop models are potentially useful tools to support analyses of the effects of climate and crop and soil management practices on crop production and the environment (e.g. carbon sequestration and greenhouse gas emissions or the leaching of agro-chemicals). However, it is not clear whether current generation models can be used to simulate long-term trends in crop production and the environmental impacts induced by changes in climate or land use because they do not consider the effects of soil structure dynamics at seasonal to decadal  (e.g. root growth, activity of macro-fauna) and centennial time scales (e.g. changes in organic matter content) on soil hydraulic functions, hydrological processes, crop growth and carbon cycling.

Here, we present a new soil-crop model that accounts for the interactions between soil structure dynamics, carbon cycling, soil physical and hydraulic properties, soil water balance and crop growth. The importance of soil structure dynamics is illustrated by long-term simulations of soil organic matter storage, soil water balance components and crop yields for a field site in central Sweden under climate change and contrasting management practices (organic amendments and crop varieties with an enhanced allocation of carbon to roots).

How to cite: Jarvis, N., Coucheney, E., Larsbo, M., Lewan, E., and Meurer, K.: Coupled modelling of soil structure dynamics, carbon cycling, hydrological processes and crop production, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12683,, 2023.

Posters virtual: Thu, 27 Apr, 08:30–10:15 | vHall SSS

Chairpersons: Ophélie Sauzet, John Koestel
Physical Disturbances to Soil Homogenize Bacterial Communities via Dispersal and Selection within Microaggregate Fractions
Jaimie West, Joseph Lauer, Bradley Herrick, and Thea Whitman
Poulamee Chakraborty, Andrey Guber, and Alexandra Kravchenko

O2 availability is one of the main factors influencing microbial processing of soil carbon and nitrogen and their cycling, and soil pore structure is what drives micro-scale patterns of O2 availability. The diffusivity of O2 is known to be a function of soil porosity and moisture content. However, the actual distribution of O2 in the soil is a product of dynamic interactions between physical (O2 diffusion) and microbial (O2 consumption) processes and is influenced by the soil pore structure. Measurements of gas diffusivity can be achieved via several laboratory techniques, while the determination of O2 consumption by microorganisms is challenging. The objectives of this study are, first, to propose a method for measurement of microbial O2 consumption under steady-state conditions in saturated soil and near saturated soil, and, second, to quantify the rate of O2 consumption in soil materials with contrasting pore structures but similar microbial compositions. The proposed method is based on Fick’s second law of diffusion, given as , where R(z) is an O2 consumption term, C is the concentration of O2, and Ds is the effective molecular diffusion coefficient of O2. The equation was solved for R(z) under steady-state conditions (near saturated soil) where the flux (J)=0. Two soil materials with contrasting pore structures, namely dominated by > 30 μm Ø pores (i.e., large-pore soil) and by < 10 μm Ø pores (i.e., small-pore soil), were prepared. The O2 profile was measured to the depth of 1 cm in the two materials under saturated and near-saturated conditions using O2 microsensor (Unisense, Aarhus, Denmark). As expected, the O2 diffusion was higher in large-pore soil as compared to the small-pore soil, however, the estimated rate of volumetric O2 consumption was also higher in the large-pore soil as compared to the small-pore soil. This finding supports the notion that large pores provide a better micro-environment for soil microorganisms stimulating their activity with subsequent increases in O2 consumption. Our ongoing work builds on these findings and explores the rate and spatial distribution patterns of O2 diffusion and microbial O2 consumption in soils with contrasting pore structures in the presence of plant residues.

How to cite: Chakraborty, P., Guber, A., and Kravchenko, A.: Influence of soil pore structure on the rate of microbial oxygen consumption, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9129,, 2023.