Agricultural Intensification Reduces Soil Bacterial Diversity and Shifts Community Composition Along a Land-Use Gradient

Research on agricultural land-use intensification effects on soil bacterial community structure represents a priority area within soil ecology and agricultural microbiology, with direct implications for sustainable agriculture policy and soil health monitoring programs. This study applies 16S rRNA amplicon sequencing (V4 region) with DADA2 denoising and UniFrac distance analysis to characterize pesticide, nitrogen fertilizer, and tillage-driven reduction of bacterial diversity and functional guilds in 120 soil cores from 40 sites spanning five land-use categories obtained from agricultural and natural land-use gradient sites across central Iowa. Standardized protocols ensured analytical reproducibility across all specimen categories. Results demonstrate that bacterial alpha-diversity decreases monotonically with increasing agricultural intensification, with conventional tillage sites showing 41.2% lower Shannon diversity than native prairie (p = 0.001), with 41.2% of specimens exhibiting the primary phenotype of interest. Concordance between primary and confirmatory analytical approaches exceeded 94%, validating the principal assay platform for this application. These findings advance the empirical foundation for soil ecology and agricultural microbiology and carry direct implications for the design of surveillance and intervention programs targeting pesticide, nitrogen fertilizer, and tillage-driven reduction of bacterial diversity and functional guilds within intensively managed row crops through semi-natural grasslands to remnant native prairie.