Observing the invisible: X-ray CT for plant–microbe interactions

Plant–microbe interactions are inherently spatial, yet the physical structure of the soil and rhizosphere is rarely treated as a mechanistic variable in experimental design. X-ray computed tomography (X-ray CT) enables nondestructive, three-dimensional, and time-resolved imaging of intact root–soil systems, providing direct access to the structural context in which plant–microbe interactions occur. Rather than a secondary imaging technique, X-ray CT can offer a wealth of data as a primary experimental platform for future plant–microbe research. Here, we highlight key structural traits that X-ray CT can quantify and discuss how they may shape microbial behaviour, plant immune responses, and disease outcomes. We expand on how X-ray CT could be employed in future to provide a framework to disentangle direct microbial effects from indirect, structure-mediated feedbacks. For breeding and management, it could enable selection for root traits and soil practices that engineer favourable microhabitats rather than targeting organisms in isolation. Despite this potential, broader adoption will require overcoming current limitations related to access to instrumentation, analytical expertise, and the integration of structural data with biological measurements. Overall, we suggest that resolving these issues will enable the integration of X-ray CT-derived structure with molecular, microbiome, and modelling approaches to enable the development of digital rhizospheres, offering a pathway from descriptive observations to predictive, structure-aware in silico frameworks in plant–microbe research.