While topography can infer erosion potential, the practice of conventional agronomic management can trigger accelerated erosion and pose major threats to soil assets such as biodiversity. The majority of farmlands in Upper-Eastern Ghana are moderately hilly and highly susceptible to erosion. This study pioneered the comparative and interactive effects of topography and conventional versus conservation agriculture practices (reduced tillage, main crop and cover crop, crop residue retention vs. removal) in treatments amended with 0, 40, and 80 kg ha−1 N on soil physicochemical properties and microbiota. Topography imposed profound shifts in soil physiochemical properties and prokaryotic community structure. Foot-slope soils harbored higher prokaryotic richness and diversity compared to the up-slope. Bacillaceae (28.95%) and anaerobic bacteria increased in relative abundance in foot-slope soils, while Micrococcaceae (25.79%) gained prominence in up-slope soils. The effect of tillage was significant in foot-slope while crop rotation was influential in up-slope soils on structuring the prokaryotic community. The interactive effect of slope × tillage was significant in altering soil physiochemical properties, but not prokaryotic community structure. Variation in prokaryotic community composition was explained by soil physiochemical properties (14.5%), elevation as a proxy for topography (11.3%), and spatial distance (10.8%), but rather weakly overall by agronomic practices. Among the soil physicochemical properties, pH, clay content, total C%, volumetric water content, temperature, cation exchange capacity, and NO3−-N were relevant factors influencing the soil microbiota. Geomorphic and soil edaphic properties appeared to interact and were the primary triggers of variation in soil microbiota and their responses to the range of agronomic practices that incorporated conservation management outcomes
