Transcriptome and functional analysis reveal the drought-alleviating ability of <i>Bacillus</i> on <i>Paeonia lactiflora</i> Pall

Bacillus is a beneficial soil microorganism that enhances plant growth and stress resistance, yet its mechanism in boosting drought resistance remains unclear. This study explored its role in enhancing herbaceous peony (Paeonia lactiflora) drought resistance via gradient soil moisture treatments (T0: 75%±5%; T1: 55%±5%; T2: 35%±5%; T3: 15%±5%). Bacillus significantly improved P. lactiflora drought resistance, especially at T2 and T3 stages, alleviating drought damage by increasing photosynthetic efficiency, antioxidant enzyme activity, and osmolyte accumulation, with abscisic acid (ABA) as a core functional component. To clarify the molecular mechanisms underlying this improvement, we performed transcriptome sequencing of P. lactiflora at the T2 and T3 stages, as well as Weighted Gene Co-expression Network Analysis (WGCNA). We identified key modules linked to Bacillus action, with WRKY transcription factors as dominant hub genes. Among these, the P. lactiflora WRKY transcription factor 70 (PlWRKY70) showed high induction by Bacillus or drought and the highest module membership (kME) in the core module. Notably, Bacillus enhanced drought resistance in P. lactiflora by upregulating PlWRKY70. Overexpressing PlWRKY70 reduced hydrogen peroxide (H₂O₂), superoxide anion (O₂·⁻), and stomatal aperture, whereas silencing PlWRKY70 produced the opposite effect, and this upregulation by Bacillus further promoted reactive oxygen species (ROS) scavenging and stomatal closure. Overall, this study reveals the physiological and transcriptional changes of P. lactiflora during Bacillus-enhanced drought resistance, identifies multiple key candidate genes responsive to Bacillus, and provides theoretical support for the popularization and application of Bacillus-based biological agents.