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...

Hydraulic redistribution (HR) by woody vegetation has been proposed as a potential water source for crops in intercropped systems. The native woody shrub, Guiera senegalensis J.F. Gmel, grows in the fields of farmers across the African Sahel and has shown profound yield benefits to associated pearl millet (Pennisetum glaucum) crops, especially in drought years. We tested whether this benefit resulted from the shrubs performing hydraulic redistribution (HR) with pearl millet using some of this HR water. During an experimentally imposed drought, an enriched deuterium (2 H) water tracer applied to 1 m deep roots of G. senegalensis shrubs was detected (2 H ≥ +300‰) in aboveground stems of intercropped millet within 12-96 h of tracer introduction. The only viable path for the 2 H-enriched H 2 O into millet was via HR by the shrubs, which confirmed active HR during the time when growing millet was under severe drought stress. Millet biomass production when intercropped with shrubs was over 900% greater than crops grown without shrubs present. Improvement of growing conditions previously found near shrubs cannot fully account for the benefit to associated millet under extreme drought stress without considering the positive impact of the transfer of HR water. This finding illuminates HR and water transfer as an important mechanism in a successful agroforestry system in a region where food security is a serious issue.

Throughout the Sahel, food insecurity remains a persistent threat. A few studies have shown that 22 Piliostigma reticulatum, a dominant native shrub in parklands from Senegal to Sudan,can positively impact crop yields. However, there are no experiments that measure whether this species can stabilize long-term crop productivity under erratic rainfall. Therefore, an 11-year study of an optimized P. reticulatumintercropping system(1000 shrubs ha-1 with annual coppiced residue soil amendments)was initiated in 2004 in Senegal, West Africa to determine its impacts on crop productivity and soil quality. The experiment was a split-plot factorial design with the main plot shrubs (with and without) and the subplot fertilizer rate (0, 0.5, 1, and 1.5 times the recommended N-P-K rate) with an annual groundnut (Arachis hypogaea) and pearl millet(Pennisetum glaucum) crop rotation. Yield, biomass, soil carbon, and soil and plant nutrient data from 2011-2015 were compared with data from 2004-2007. The presence of shrubs increased millet and groundnut yield from 2011-2015 and rainfall water use efficiency (WUE) between 2004 and 2015. Without fertilizer addition, the shrub plots had approximately 2 times greater millet yield throughout the duration of this experiment. The presence of shrubs also improved soil quality, as evidenced by significantly greater C in the fraction <53 µm and total C in shrub over non-shrub plots. Thus, P. reticulatum intercropping promotes C sequestration. In addition, five macronutrients (N, K, Ca, Mg, S) and two micronutrients (Mn and Cu) were significantly greater in the shrub plots. The results provide strong evidence that intercropping with P. reticulatum is an ecological agroforestry system for the Sahel that can remediate soils, increase crop yields, and buffer climate change.

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