Long-term maize-Desmodium intercropping shifts structure and composition of soil microbiome with stronger impact on fungal communities

Abstract Purpose Push–pull is an intercropping technology that is rapidly spreading among smallholder farmers in Sub-Saharan Africa. The technology intercrops cereals with Desmodium to fight off stem borers, eliminate parasitic weeds, and improve soil fertility and yields of cereals. The above-ground components of push–pull cropping have been well investigated. However, the impact of the technology on the soil microbiome and the subsequent role of the microbiome on diverse ecosystem benefits are unknown. Here we describe the soil microbiome associated with maize— Desmodium intercropping in push–pull farming in comparison to long-term maize monoculture. Methods Soil samples were collected from long-term maize— Desmodium intercropping and maize monoculture plots at the international centre for insect physiology and ecology (ICIPE), Mbita, Kenya. Total DNA was extracted before16S rDNA and ITS sequencing and subsequent analysis on QIIME2 and R. Results Maize— Desmodium intercropping caused a strong divergence in the fungal microbiome, which was more diverse and species rich than monoculture plots. Fungal groups enriched in intercropping plots are linked to important ecosystem services, belonging to functional groups such as mycorrhiza, endophytes, saprophytes, decomposers and bioprotective fungi. Fewer fungal genera were enriched in monoculture plots, some of which were associated with plant pathogenesis and opportunistic infection in humans. In contrast, the impact of intercropping on soil bacterial communities was weak with few differences between intercropping and monoculture. Conclusion Maize— Desmodium intercropping diversifies fungal microbiomes and favors taxa associated with important ecosystem services including plant health, productivity and food safety.