Rational Design of an Arid Plant-Derived Endophytic Consortium Improves Crop Performance under Controlled Conditions

Endophytic bacteria from arid medicinal plants represent a promising source of stress-adapted, plant growth-promoting (PGP) microorganisms. Here, we investigated the cultivable endophytic microbiota of Peganum harmala using both nutrient-rich and diluted media to maximize taxonomic recovery. Isolates were dominated by Bacillota and Gammaproteobacteria, with higher diversity in roots than in shoots. Venn analysis revealed a shared core fraction between compartments, forming the basis for consortium assembly. Nine representative strains belonging to Phyllobacterium, Bacillus, Brevibacillus, Burkholderia, Ralstonia, and Amycolatopsis were selected for functional screening. Pairwise antagonism assays showed high compatibility among Bacillus-related strains, whereas certain taxa exhibited inhibitory interactions, guiding rational consortium design. Functional characterization demonstrated complementary PGP traits, including nitrogen-related activity, phosphate, potassium, and silicate solubilization, siderophore and indole-3-acetic acid production, and ammonia production. No single isolate performed optimally across all traits, supporting a consortium-based strategy. A synthetic bacterial consortium (C2), reconstructed from the core endophytic microbiota using compatibility-guided selection, was evaluated in two crop systems. In vitro flax germination assays showed accelerated radicle emergence and improved vigor index, particularly with C2. Under greenhouse conditions, C2 significantly enhanced flax shoot and root biomass, root architecture, leaf area expansion, and photosystem II performance in sterile soil. In faba bean under natural soil, C2 increased leaf number (p = 0.02) relative to the control. These results indicate that consortia derived from core endophytes of arid medicinal plants can promote plant growth across diverse crops and soil contexts, although effects remain context-dependent and require rigorous field validation. IMPORTANCEEndophytic bacteria can serve as sustainable bioinoculants to enhance crop performance under stress conditions. This study demonstrates that the core microbiota of the arid medicinal plant Peganum harmala can be rationally assembled into a functionally complementary consortium that improves germination, nutrient acquisition, and whole-plant physiological performance in flax and faba bean. By combining compatibility-guided assembly with functional screening, we show that consortium-based strategies may outperform single-strain inoculants. These findings provide insight into the development of scalable, plant growth-promoting microbial consortia and highlight the importance of testing microbial inoculants under multiple environmental contexts to ensure consistent benefits.