Genomic and Functional Characterization of Sunflower Endophytes Reveals Mechanisms of Drought Tolerance and Growth Promotion

Drought severely limits sunflower ( Helianthus annuus L.) productivity, necessitating sustainable microbial strategies to enhance plant resilience. Endophytic bacteria modulate plant stress responses through diverse plant growth‐promoting (PGP) traits. This study characterized Pseudomonas protegens M4 and Citrobacter braakii M34 and evaluated their individual and combined effects on sunflower drought tolerance. Greenhouse experiments assessed inoculation with M4, M34, and their consortium (M4 + M34) under optimal (100% field capacity, FC) and drought conditions (75%–25% FC). Initial taxonomic identification based on 16S rRNA gene sequencing was further refined using whole‐genome sequencing (WGS) for high‐resolution classification and functional analysis. Genomic annotation and antiSMASH analysis revealed key PGP pathways in both strains, including enzymes involved in ethylene regulation, phosphate solubilization, biosynthesis of auxin‐like compounds, osmoprotectant production, and reactive oxygen species detoxification, alongside shared and strain‐specific secondary metabolite gene clusters. Under drought conditions, M4 primarily enhanced growth‐related traits such as shoot development and leaf area, whereas M34 was associated with physiological stress tolerance indicators. The consortium M4 + M34 exhibited synergistic effects, significantly increasing the chlorophyll content, relative water content, and proline accumulation while reducing electrolyte leakage. Principal component analysis further confirmed the consortium's superior performance. These findings highlight the potential of genomically and functionally characterized endophytic bacterial consortia as effective bioinoculant strategies for improving sunflower productivity under water‐limited conditions.