High species dispersal of plant-beneficial bacteria in farmland soils across Eastern China

Plant-beneficial bacteria (PBB) play a critical role in sustaining soil health and enhancing crop productivity through nutrient mobilization, pathogen suppression, and stress resilience. Yet, how environmental factors shape the biogeography and assembly of PBB in agricultural soils remains unclear. To fill this knowledge gap, we conducted a large-scale study across eastern China farmland to investigate: (i) the diversity, composition, and spatial distribution of PBB, and (ii) the key environmental drivers and mechanisms governing PBB community assembly. We found that plant growth-promoting (PGP), biocontrol (BIOC), and stress resistance (SR) functional groups accounted for 4.6–13.2%, 0.7–4.8%, and 0.1–1.3% of total bacterial community, respectively. The α-diversity of total bacteria was positively correlated with that of PBB, suggesting that overall microbial richness supports beneficial taxa. Soil pH acted as the primary driver of β-diversity for SR and BIOC, while mean annual precipitation (MAP) was the main factor influencing PGP β-diversity. Community assembly analysis revealed that species replacement contributed more to PBB β-diversity than richness differences. Mechanistically, homogeneous selection was the dominant process structuring PGP, BIOC, and SR assemblages, whereas dispersal limitation primarily governed the total bacterial community. Accordingly, all three PBB functional groups showed higher dispersal capacity and contained more generalist taxa than the total bacteria. The high abundance and broad distribution of PGP, BIOC, and SR underscored their potential ecological benefits, which are modulated by key environmental factors such as soil pH and precipitation. Our findings highlight key environmental filters for PBB assembly and identify widely distributed, generalist taxa, providing a framework for the targeted screening of regionally adapted microbial inoculants.