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Soil structure creates spatial heterogeneity that shapes ecosystem functions, including water retention and root colonization. Chernozems – soils characterized by exceptionally stable aggregation resulting from millennia of root-soil co-evolution – offer a unique model to investigate how aggregate-scale pore architecture controls plant responses to drought. Using soil microcosms (4 × 10 cm, ~80 g soil) with aggregates from Native Steppe and Arable Chernozems, we established six experimental treatments (3 aggregate sizes × 2 soil types) with three replicates each. Root-soil dynamics were tracked through repeated X-ray computed tomography (Neoscan N80, Belgium) at 16 µm resolution. Imaging was synchronized with plant developmental stages – germination, first leaf, and third leaf stage at permanent wilting point – yielding a total of 54 soil tomograms for analysis.Preliminary processing of the data reveals distinct pore network architectures across aggregate size classes. Small aggregates exhibited low CT-visible porosity (24%) with high solid phase connectivity (6.60 mm⁻³), while medium aggregates showed moderate porosity (39%) with lower connectivity (0.64 mm⁻³), and large aggregates had the highest porosity (49%) but the lowest connectivity (0.51 mm⁻³). This structural gradient directly controlled root colonization: solid phase connectivity showed a strong negative correlation with root volume growth (r = −0.76), suggesting that matrix mechanical cohesion, rather than pore characteristics alone, limits root expansion. Medium aggregates – which naturally dominate in undisturbed steppe soils – provided optimal conditions for root development, with 90% greater root surface expansion compared to small aggregates. Root sphericity decreased 3–4 times more in medium aggregates (−0.14) than in small aggregates (−0.04), indicating greater architectural plasticity critical for water acquisition. Importantly, our preliminary results also show that medium aggregates provided the greatest drought resistance: plants in these microcosms reached the permanent wilting point latest, suggesting that this aggregate fraction optimizes both root development and water availability over time.These findings demonstrate that native Chernozem aggregate structure represents an optimized spatial configuration balancing root accessibility with water retention. The strong coupling between aggregate-scale heterogeneity and root response suggests that tillage-induced disruption of natural aggregate distributions may compromise this evolutionary optimization. Our approach – combining high-resolution CT with growth stage-synchronized imaging – offers a framework for quantifying how spatial heterogeneity translates into ecosystem-relevant soil functions. Data processing is ongoing, and final results will include expanded replication and additional root morphometric parameters.