X-ray tomography imaging and the image processing and analysis of the datasets created have become critical components of the science behind the undisturbed visualisation of soil inner structure. A new image segmentation algorithm able to extract multiple regions of interests from challenging image stacks of soil cores with complex geometry is presented. The method was tested against a dataset of soil cores and demonstrated robustness and superior performance against widely used state-of-the-art methods, thus paving the way for the automated analysis of X-ray tomography datasets.

In this paper the capabilities of two different contrast agents, phosphomolybdic acid and silver nitrate, to stain soil particulate organic matter (POM) are tested through X-ray tomography in addition to different segmentation approaches. Results showed that contrast agents increased X-ray linear attenuation coefficient of POM while manual thresholding resulted in the best performances to separate POM from other soil phases.

Myxodiaspores produce mucilage while germinating. Our work shows that a mucilage capsule extruded by chia (Salvia hispanica L.) seeds alters soil structure during the first stages of germination and strongly binds soil. This provides a microenvironment of altered pore diameter and high aggregate stability around the diaspore, and characterises a transient but crucial time of crop production when the soil is totally or partly bare after sowing and when physical conditions around the seed are relevant to stability, germination and plant–microorganism relations.

The tepetates are indurated subsoil horizons with different hypothesis of its origin. Observation of undisturbed samples in 2D and 3D showed distinct stages of its formation. As we could see from computed tomography, the small homogeneously distributed pores were formed during the primary compaction, meanwhile large pore crack pores appeared later. The clay coating found in this sections were infilling those large pore cracks after they appeared and participated in secondary compaction of tepetates.

The formation of boreal Retisol is reflected in the morphology of its horizons, among other in the pore space distribution. In this soil the fragic EBx horizon has mainly closed micropores, a possible explanation is the absence of turbation processes. Meanwhile the porosity of upperlying and underlying horizons was formed by turbation and desiccation cracking respectively.

Water retention in granular soils is a key mechanism for understanding transport processes in the vadose zone, for various applications from agronomy to hydrological and environmental sciences. In this paper, we predict the drainage water retention curve by applying the voxel percolation method using micro computed tomography imaging. The voxel percolation method showed a good capability to predict the water retention curve.

Water transfer in soils strongly depends on permeability. Recent advances in 3D imaging based on X-ray tomography allow estimation of this parameter using numerical simulations of flow in realistic pore geometry. In this paper, the effect of scan resolution on the permeability estimate is analysed for a reference sand and a virtual pack of spheres. A criterion based on the pore size distribution is proposed to assess if a scan is suitable for permeability computation.

Studying of macropores and preferential flow in mountain forest areas are crucial for reducing occurrence of surface runoff and soil erosion. This study aimed to characterise macropore structures and corresponding preferential flow patterns under contrasting human disturbance levels, and found that human disturbance significantly decreased soil macropores and preferential water flow. The human disturbance should be reduced for conservation of soil and water.

We analysed orchard management effects on carbon content and architecture of pores >92 µm in topsoils under integrated and organic kiwifruit. Significant relationships between soil parameters and indicators of preferential flow verified that structural parameters derived by computed tomography can predict solute transport. The organic orchard’s topsoil was a superior filter due to changed architecture related to higher carbon content.

Volcanic soils are among the most fertile soils in the world but their unique properties can be lost through cultivation. Laboratory and field techniques were employed to investigate the hydrodynamic properties and pore architecture of two types of soils derived from volcanic ash and ejecta. Tillage negatively affected the total porosity and macropore size along with an increase in the number of isolated macropores. The maize–wheat rotation also affected the hydrodynamic properties compared with maize monoculture. Sustainable agricultural practices should include minimum tillage, reducing periods when soil is bare and preferring maize–fallow rotation allowing natural vegetation growth.

Understanding of mass and energy transport processes in soil through pore networks is important for assessing environmental risks such as greenhouse gases or toxic volatile compounds and optimisation of remediation techniques at contaminated sites. The manuscript deals with the prediction of mass transport parameters by using X-ray CT-derived pore network structure with good accuracy. Accurately linking the pore structure information and mass transport parameters will allow easy and rapid quantification of important soil functional properties.

We hypothesised that topsoil structure would change under intensification of arable production. We analysed gas transport and pore-network characteristics under different tillage and irrigation treatments. Differences in pore-network structure were attributed to carbon depletion and mechanical disturbance through intensive tillage. Correlations between structural characteristics and gas transport parameters suggest that X-ray computed tomography could be useful for predicting gas transport.

Grazing of forage crops in situ can lead to high emissions of nitrous oxide, a potent greenhouse gas, and leaching of nitrate to water, both of which are environmental pollutants of global concern. The combination of animal treading on cultivated soil in simulated winter grazing conditions changes the soil aeration conditions increasing nitrous oxide emissions, but reduces the amount of nitrate that subsequently leaches. Crop establishment and grazing management practices should focus on avoiding soil compaction under wet conditions, especially on cultivated soil.

Soil water repellency creates a skin on the soil surface, preventing water being absorbed into the soil, depriving plants and microbes of critical moisture and slowing growth. The mechanisms of the development of repellency remain obscure; however, through measurement of soil enzyme activities, some key enzymes involved have been identified. Understanding the action of these enzymes and how they relate to repellency will allow development of treatments to remediate soil water repellency and improve soil quality.