Partitioning the effects of coffee-Urochloa intercropping on soil microbial properties at a centimeter-scale

Conservation farming and crop diversity increase soil health, organic matter content, and soil microbial activity. However, the design and implementation of sustainable practices often lack a detailed understanding of their impacts on microbial communities in soil. Here, we studied the effects of an Arabica coffee (Coffea arabica) – Brachiaria (Urochloa spp.) intercropping system on soil microbial properties by partitioning at the centimeter-scale the topsoil layers. In particular, we collected and analyzed four soil layers in a vertical stratification gradient of 0–2.5 cm (layer 1), 2.5–5.0 cm (layer 2), 5–10 cm (layer 3), and 10–15 cm (layer 4). Soil samples were subjected to chemical analysis, bacterial community profiling, and quantification of microbial enzymatic activity for β-glucosidase and acid-phosphatase, in addition to the quantification of N-fixation and P-solubilization gene abundances. We found that intercropping increased acid-phosphatase activity at layer 1, β-glucosidase activity at layers 2 and 3, and the amount of soil organic matter and total magnesium at layers 2 and 3. Intercropping increased the relative abundance of the N-fixation gene at layer 3 and bacterial diversity at layers 1 and 3. Overall, intercropping significantly changed the soil bacterial community structure and resulted in a more interconnected co-occurrence network (i.e., greater node connectivity, network density, and lower edges average path length). Taken together, this study provides evidence for the positive impact of intercropping in the soil at a centimeter-scale vertical stratification. It corroborates the notion that plant diversity stimulates microbial activity and species interactions in soil. •Intercropping had positive impacts on soil organic matter and microbial activity.•Soil coverage shifted soil bacterial community structure, richness, and diversity.•nifH gene abundance increased at a specific soil depth in the intercropping system.•Intercropping resulted in a more complex co-occurrence network of bacterial taxa.