Soil microorganisms in a temperate agroforestry system are shaped by soil depth and fertilization rate

Abstract Temperate agroforestry can offer numerous environmental benefits over open croplands, including improved soil health. Recent studies suggest that adequate nutrient management (i.e., reduced fertilizer inputs) in agroforestry systems may even further improve their environmental performance. We conducted a 4-year fertilization experiment (regular vs. reduced mineral fertilization) in a paired short-rotation poplar alley-cropping and a reference open cropland system and assessed microbial abundance, bacterial community composition, as well as abundance of functional genes involved in N cycling in topsoil and subsoil. Within the alley-cropping system, soil samples were collected along transects spanning from the tree strips into the crop alley. Tree strips altered bacterial community composition and promoted fungal abundance in both topsoil and subsoil, likely due to the absence of soil management. Soil depth was the largest driver of bacterial community composition, which we relate to changes in resource availability with soil depth. Reduced fertilization did not alter microbial abundance and bacterial diversity across management systems, while the relative abundance of several bacterial taxa was affected by the fertilization rate. For instance, in both management systems, reduced fertilization decreased the relative abundance of Nitrospira spp. in topsoil. Additionally, their abundance in topsoil was lower in the unfertilized tree strips than in the fertilized agroforestry crop alley and open cropland, suggesting that mineral fertilizer promotes these nitrifiers in topsoil. Overall, although microbial abundance typically benefits from fertilizer inputs, the reduced fertilization treatment did not compromise soil microbial abundance nor bacterial diversity, indicating the absence of trade-offs between adequate nutrient management and soil microbial communities.