The role of inherited characteristics from parent materials in shaping bacterial communities in agricultural soils

Parent materials are crucial in soil formation and development, but their importance in shaping soil bacterial communities after thousands of years of soil formation remains unknown, especially in agricultural soils. To resolve the influence of underlying features inherited from parent materials on soil microbiome, the microbial community in 197 agricultural soils with long-term crop cultivation history and nonagricultural reference soils from four major types of soils in China, i.e., quaternary red clay soils, tertiary red sandstone soils, alluvial soils and black soils, were analyzed and compared. We found that different types of soils supported distinct bacterial communities. The characteristics inherited from parent materials explained more of the variation (31.47%) in bacterial community structure than the selected variables regulated by soil management (1.63%) and the climate condition (1.10%). Only 9.0% of total bacterial amplicon sequence variants (ASVs) which contributed, on average, 47% of the total bacterial abundances in a given agricultural soil, were shared by all soil types. These abundant common ASVs were closely related to agricultural practices, suggesting a strong enrichment effect of a small number of core taxa by long-term crop cultivation. In contrast, approximately 55.6% of ASVs with low relative abundance were specific to soil type. These specific groups were closely associated with the distinctive features of soil type, implying that they represent unique populations selected by the parent material features during pedogenesis. Collectively, soil type may have a strong selective pressure on the bacterial communities in matured agricultural soils, leading to a large pool of specific taxa with limited environmental occurrence. Whilst a small number of core taxa achieve high abundances by responding to long-term crop cultivation.