Driving Effects of Soil Microbial Diversity on Soil Multifunctionality in Carya illinoinensis Agroforestry Systems

Sustainable soil management requires striking a balance between productivity and soil health. While agroforestry practices are known to improve soil health and ecosystem functions, the contribution of microbial diversity to maintaining multifunctional soil processes in pecan (<i>Carya illinoinensis</i>) cultivation has yet to be fully elucidated. This study examined microbial diversity, soil functions, and multifunctionality across different pecan intercropping setups. We compared a monoculture pecan plantation with three agroforestry models: pecan-<i>Paeonia suffruticosa</i>-<i>Hemerocallis citrina</i> (CPH), pecan-<i>P. suffruticosa</i> (CPS), and pecan-<i>P. lactiflora</i> (CPL). We employed high-throughput sequencing (16S and ITS) to determine the soil bacterial and fungal communities and analyzed the species diversity, extracellular enzyme activities, and physicochemical properties. Soil multifunctionality (SMF) was evaluated using 20 indicators for nutrient supply, storage, cycling, and environmental regulation. Agroforestry increased soil fungal diversity and improved multifunctionality when compared to monoculture. The CPS and CPH models were the most beneficial, increasing multifunctionality by 0.74 and 0.55 units, respectively. Structural equation modeling revealed two key pathways: bacterial diversity significantly enhanced nutrient cycling and environmental regulation, whereas fungal diversity primarily promoted nutrient cycling. These pathways together delivered clear gains in multifunctionality. Random forest analysis identified key predictors (total nitrogen, total carbon, available potassium, β-1,4-N-acetylglucosaminidase, and alkaline phosphatase), highlighting the joint importance of nutrients and microbial enzymes. Our results demonstrate that selecting species in pecan agroforestry alters microbial communities and activates key functions that support soil health and long-term resilience. Hence, pecan agroforestry maintains SMF through microbial processes, with CPS showing the strongest effect. These results can inform species selection and encourage broader testing for resilient, biodiversity-based farming practices.