Both inherent soil properties and management practices shape soil microbial communities under prolonged organic management

The soil microbiome is recognized as a key component of soil health; however, microbial community responses to agricultural management can be inconsistent and context dependent. Here, we investigated the connections between soil microbial communities, soil properties, and agricultural practices in the Driftless Region of southwestern Wisconsin, spanning 128 fields that have been under organic management for varying lengths of time (from 3 up to 51 years). We employed principal component analysis (PCA) and structural equation modeling (SEM) to uncover the effects of tillage, time under organic management, alfalfa use, and cover crop (CC) use on total carbon (C), nitrogen (N), and pH while examining their direct and indirect effects on bacterial biomass, bacterial diversity, relative abundance of arbuscular mycorrhizal fungi (AMF), and fungal diversity. Our multivariate analysis found that both bacterial and fungal community compositions were highly varied between fields that were recently transitioned to organic management but converged to a consistent state under prolonged organic management (> 20 years). SEM suggested that bacterial biomass increased with continuous alfalfa use, likely via improved nitrogen availability. Frequent tillage significantly reduced the proportion of AMF, limiting proliferation due to disturbance. Additionally, fungal diversity increased in acidic soils, while bacterial diversity was greater in neutral or basic soils. This study demonstrates how organic management in dairy forage systems likely shapes microbial community composition, especially through tillage and alfalfa use. These findings confirm the previous understanding of soil disturbance and soil chemical effects on soil microbial communities and caution that time under organic management per se should not be expected to lead to predictable changes in soil conditions. Rather, the direct and indirect consequences of specific management practices must be understood to develop cropping systems that build soil health over time.