Vegetation-Driven Differentiation of Soil Bacterial and Fungal Diversity: Distinct Edaphic Determinants in Atractylodes japonica Cultivation Systems

As key drivers of soil biogeochemical cycles, soil microbial communities play essential roles in maintaining soil fertility, nutrient cycling, and plant growth. In this study, high-throughput sequencing of 16S rRNA and ITS genes was used to investigate the diversity, the composition, and the driving factors of bacterial and fungal communities in bulk soils across four soil groups collected from different vegetation covers (forest soil (FS), soybean field (PGS), and two Atractylodes japonica cultivation soils (ALO and ALR)) under identical climatic conditions. The results showed that the bacterial α-diversity remained stable across all the vegetation types, whereas the fungal α-diversity and richness were more sensitive to the vegetation type, with the PGS generally exhibiting lower Shannon and Chao1 indices. The β-diversity analysis revealed significant differences in the microbial community structure among the vegetation types, with a stronger effect on fungi (R2 = 0.737, p = 0.001) than on bacteria (R2 = 0.493, p = 0.001). At the phylum and genus levels, the fungal communities displayed more pronounced shifts than the bacterial communities, which remained relatively stable. A redundancy analysis indicated that the soil chemical properties significantly shaped the microbial community structure (p = 0.002). The microbial communities in the A. japonica soils (ALO and ALR) were primarily driven by pH, available phosphorus, and available potassium, while the FS and PGS communities were more strongly influenced by soil organic carbon, total nitrogen, and nitrogen forms (NH4+-N and NO3−-N). The Spearman correlation and functional prediction analyses further confirmed that the key soil factors differentially regulated the abundance and ecological functions of the dominant microbial taxa. These findings demonstrate the vegetation-specific assembly of soil microbial communities and highlight the distinct edaphic drivers associated with A. japonica cultivation, providing a scientific basis for soil health management and the sustainable cultivation of this medicinal plant.