Ziziphus lotus (L.) Lam. (Rhamnaceae), a key shrub species native to North Africa, is commonly found in arid and semi-arid regions. Renowned for its resilience under harsh conditions, it forms vegetation clusters that influence the surrounding environment. These clusters create microhabitats that promote biodiversity, reduce soil erosion, and improve soil fertility. However, in agricultural fields, Z. lotus is often regarded as an undesirable species. This study investigated the bacterial diversity and community composition along spatial gradients around Z. lotus patches in barley-planted and non-planted fields. Using 16S rRNA gene sequencing, 84 soil samples were analyzed from distances of 0, 3, and 6 m from Z. lotus patches. MiSeq sequencing generated 143,424 reads, representing 505 bacterial ASVs across 22 phyla. Alpha-diversity was highest at intermediate distances (3 m), while beta-diversity analyses revealed significant differences in community composition across distances (p = 0.035). Pseudomonadota dominated close to the shrub (44% at 0 m) but decreased at greater distances, whereas Bacillota and Actinobacteriota displayed distinct spatial patterns. A core microbiome comprising 44 ASVs (8.7%) was shared across all distances, with the greatest number of unique ASVs identified at 3 m. Random forest analysis highlighted Skermanella and Rubrobacter as key discriminatory taxa. These findings emphasize the spatial structuring of bacterial communities around Z. lotus patches, demonstrating the shrub’s substantial influence on bacterial dynamics in arid ecosystems.

Ziziphus lotus (L.) Lam., (Rhamnaceae) a resilient shrub native to Moroccan’s arid regions, functions as a keystone species by creating microhabitats that buffer temperature extremes, retain soil moisture, and accumulate organic matter. However, its role in structuring soil fungal diversity and community composition in these environments remains largely unexplored. This study investigated the spatial distribution of fungal communities associated with Z. lotus in barley-planted and non-planted fields. Soil samples were collected at 0, 3, and 6 m from shrub clusters during the barley harvest. The fungal community was dominated by Ascomycota (93.5%). Alpha diversity indices (Shannon–Wiener and Simpson) were significantly higher near shrub bases (0 and 3 m) compared to more distant soils (6 m), indicating a clear decline in diversity with distance (0 m vs. 6 m: p = 0.0012; 3 m vs. 6 m: p = 0.0007). Soil physicochemical parameters, including calcium carbonate content, nitrate, and salinity, significantly influenced fungal diversity (p ≤ 0.05). Beta diversity analysis revealed significant spatial differentiation in fungal community composition (PERMANOVA: p = 0.001). Overall, fungal richness and diversity were highest near shrub. Genera such as Cladosporium, Fusarium, and Alternaria were more abundant near shrub bases, while taxa like Didymellaceae and Alfaria were specially restricted. Functional predictions indicated dominance of fungi with mixed trophic modes (pathotroph–saprotroph–symbiotroph), suggesting ecological plasticity. Despite barley cultivation, the fungal community structure remained largely similar between the planted and non-planted fields. Overall, our findings underscore the ecological importance of Z. lotus as a reservoir of stress-tolerant fungi and as a potential keystone species for restoring degraded arid ecosystems.