Perennial cropping systems are increasingly recognized for their potential to enhance soil functions, particularly carbon sequestration and water regulation. However, the structural mechanisms driving these improvements remain poorly understood. In this study, we investigated how ten years of Silphium perfoliatum cultivation altered soil pore architecture compared to a conventionally tilled crop rotation, and how these structural changes affect two key soil functions: soil organic carbon (SOC) accrual and near-saturated water flow.

Using X-ray microtomography, we quantified the three-dimensional pore network across cropping systems, linking structural features to SOC and hydraulic measurements.

S. perfoliatum induced a fundamentally different pore architecture, dominated by small biopores and an organic-rich porous matrix, likely shaped by roots and soil fauna. This structure was closely linked to enhanced SOC accrual in S. perfoliatum, with root-derived particulate organic matter (POM) contributing to the formation of stabilized microsites. Water flow responses were equally distinct. Despite the positive influence of continuous biopores in S. perfoliatum on water flow, the hydraulic conductivity of the topsoil was reduced − likely due to partial blocking with roots and POM. Conversely, in the crop rotation, higher conductivity was associated with abundant small pores and matrix-dominated flow, despite less favorable biopore structure.

Overall, our findings confirm that long-term perennial management leads to the formation of a functionally distinct pore architecture that regulates both carbon storage and water transport. These results highlight the importance of pore structural context in shaping key soil functions and offer mechanistic insight into the long-term benefits of perennial cropping systems.