The Topographic Template: Coordinated Shifts in Soil Chemistry, Microbiome, and Enzymatic Activity Across a Fluvial Landscape

The soil microbiome is an essential component of agroecosystems. However, managing it remains a challenge due to our limited knowledge of how various environmental factors interact and shape its spatial distribution. This study presents a hierarchical ecological model to explain the assembly of the microbiome in sloping agricultural landscapes. Through a comprehensive analysis of bacterial and fungal communities, as well as the examination of metabolic and phytopathogenic profiles across a topographic gradient, we have demonstrated that topography acts as the main filter, structuring bacterial communities. Land use, on the other hand, serves as a secondary filter, refining fungal functional guilds. Our results suggest that hydrological conditions in floodplains favor the growth of stress-tolerant bacterial communities with low diversity, dominated by Actinomycetota. Fungal communities, on the other hand, are directly influenced by land use. Long-term fallow periods lead to an enrichment of arbuscular mycorrhiza, while agroecosystems shift towards pathogenic and saprotrophic niches. Furthermore, we identify specific topographic positions that may be hotspots for phytopathogenic pressure. These hotspots are linked to certain taxa, such as Ustilaginaceae and Didymellaceae, which may pose a threat to plant health. The derived hierarchical model provides a scientific foundation for topography-aware precision agriculture. It promotes stratified management, prioritizing erosion control and soil restoration on slopes, customizing nutrient inputs in fertile floodplains, and implementing targeted phytosanitary monitoring in identified risk areas. Our research thus offers a practical framework for harnessing soil spatial variability to improve soil health and proactively manage disease risks in agricultural systems.