dThis study characterized specific changes in the millet root zone microbiome stimulated by long-term woody-shrub intercropping at different sites in Senegal. At the two study sites, intercropping with woody shrubs and shrub residue resulted in a significant increase in millet [Pennisetum glaucum (L.) R. Br.] yield (P < 0.05) and associated patterns of increased diversity in both bacterial and fungal communities in the root zone of the crop. Across four experiments, operational taxonomic units (OTUs) belonging to Chitinophaga were consistently significantly (P < 0.001) enriched in the intercropped samples, and "Candidatus Koribacter" was consistently significantly enriched in samples where millet was grown alone. Those OTUs belonging to Chitinophaga were enriched more than 30-fold in residue-amended samples and formed a distinct subgroup from all OTUs detected in the genus. Additionally, OTUs belonging to 8 fungal genera (Aspergillus, Coniella, Epicoccum, Fusarium, Gibberella, Lasiodiplodia, Penicillium, and Phoma) were significantly (P < 0.005) enriched in all experiments at all sites in intercropped samples. The OTUs of four genera (Epicoccum, Fusarium, Gibberella, and Haematonectria) were consistently enriched at sites where millet was grown alone. Those enriched OTUs in intercropped samples showed consistently large-magnitude differences, ranging from 30-to 1,000-fold increases in abundance. Consistently enriched OTUs in intercropped samples in the genera Aspergillus, Fusarium, and Penicillium also formed phylogenetically distinct subgroups. These results suggest that the intercropping system used here can influence the recruitment of potentially beneficial microorganisms to the root zone of millet and aid subsistence farmers in producing higher-yielding crops.
Subsistence farmers in the Sahel region of sub-Saharan Africa struggle with the challenges of drought, low organic matter in soils, and encroaching desertification (1). Resolving these issues is critical for improving crop yields in this region. Woody shrubs that occur naturally in farmers' fields might be used as part of an intercropping production system to improve crop yields. Two woody shrubs, Guiera senegalensis and Piliostigma reticulatum, are distributed throughout the Sahel region (2, 3). Currently, most farmers manage these shrubs by coppicing, collecting, and burning above-ground residue prior to planting crops. However, agricultural practices in the Sahel region can be adjusted to utilize shrub biomass as a natural source of fertilizer (4). Shrub residue can be added to the soil as a nutrient-rich organic amendment and decompose within an 8-month time period (5). Rhizosphere soils around amended shrubs show increased nutrient content (6), improved soil moisture profiles due to hydraulic lift (7), and a more diverse and complex microfauna soil food web (8). Intercropping with G. senegalensis (9) and P. reticulatum (10), with the incorporation of shrub residue, has also been shown to improve crop yields at two long-term field sites in Senegal...