Intercropping enhances overall soil multifunctionality and buffers functional decline in subsoil

Abstract Legume-cereal intercropping represents a key paradigm for sustainable agricultural intensification; however, the biological mechanisms driving soil multifunctionality (SMF) under these systems remain elusive. Here, we investigated SMF responses to an oat-vetch intercropping system across topsoil and subsoil profiles. Our results indicate that intercropping significantly enhanced SMF and functioned as a crucial strategy to buffer the precipitous functional decline typically observed in monoculture subsoils. Notably, while monoculture systems exhibited a sharp vertical decline in SMF (>86%) from topsoil to subsoil, intercropping significantly mitigated this reduction to 66%. Random Forest analysis identified dissolved organic carbon (DOC) as the primary abiotic predictor of SMF. Biologically, this functional enhancement was driven not merely by changes in fungal richness, but by the optimization of the fungal community structure, specifically toward a higher saprotroph-to-pathogen ratio. Structural Equation Modeling further disentangled two distinct mechanistic pathways: planting patterns stimulated SMF by increasing DOC, which reshaped the fungal community structure via host selection; conversely, soil depth constrained SMF by limiting fungal diversity through environmental filtering. These findings highlight a mechanism wherein root-derived labile carbon drives functional fungal succession. We conclude that incorporating vetch into cereal cropping systems effectively mitigates subsoil functional degradation by enriching labile carbon pools and optimizing the structural composition of the soil microbiome.