Background The need to observe roots in their natural undisturbed state within soil, both spatially and temporally, is a challenge that continues to occupy researchers studying the rhizosphere. Scope This paper reviews how over the last 30 years the application of X-ray Computed Tomography (CT) has demonstrated considerable promise for root visualisation studies. We describe how early CT work demonstrated that roots could be visualised within soils, but was limited by resolution (ca. 1 mm). Subsequent work, utilising newer micro CT scanners, has been able to achieve higher resolutions (ca. 50 μm) and enhance imaging capability in terms of detecting finer root material. However the overlap in the attenuation density of root material and soil pore space has been a major impediment to the uptake of the technology. We then outline how sophisticated image processing techniques, frequently based on object tracking methods, have demonstrated great promise in overcoming these obstacles. This, along with the concurrent advances in scan and reconstruction times, image quality and resolution (ca. 0.5 μm) have opened up new opportunities for the application of X-ray CT in experimental studies of root and soil interactions. Conclusions We conclude that CT is well placed to contribute significantly to unravelling the complex interactions between roots and soil.

The rhizosphere is the zone of soil influenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in different soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of influence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots significantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This ‘rhizosphere pore structure’ and its impact on associated dynamics are discussed.

Summary Soil systems are characterized by the spatial and temporal distribution of organic and mineral particles, water and air within a soil profile. Investigations into the complex interactions between soil constituents have greatly benefited from the advent of non‐invasive techniques for structural analysis. In this paper we present a review of the application of one such technique, X‐ray computed tomography (CT), for studies of undisturbed soil systems, focusing on research during the last 10 years in particular. The ability to undertake three‐dimensional imaging has provided valuable insights regarding the quantitative assessment of soil features, in a way previously unachievable because of the opaque nature of soil. A dynamic approach to the evaluation of soil pore networks, hydro‐physical characteristics and soil faunal behaviour has seen numerous scanning methodologies employed and a diverse range of image analysis protocols used. This has shed light on functional processes across multiple scales whilst also bringing its own challenges. In particular, much work has been carried out to link a soil's porous architecture with hydraulic function, although new technical improvements allowing the characterization of organic matter and the influence of soil biota on structural development are showing great promise. Here we summarize the development of X‐ray CT in soil science, highlight the major issues relating to its use, outline some of the applications for overcoming these challenges and describe the potential of future technological advances for non‐invasive soil characterization through integration with other complementary techniques.