Bacillus velezensis BY6 Controls Armillaria Root Rot in Poplar by Reshaping Rhizosphere–Phyllosphere Microbiomes and Inducing Systemic Resistance

<i>Armillaria solidipes,</i> the causal agent of <i>Armillaria</i> root rot, poses a severe and persistent threat to poplar forest plantations. This study evaluated the biocontrol efficacy of the endophytic bacterium <i>Bacillus velezensis</i> BY6 against this pathogen and elucidated its multimodal mechanisms of action. BY6 application significantly reduced disease severity by 37.19% at 30 days post-treatment. 16S rRNA (V3-V4) microbiome analysis revealed that BY6 reshaped both the rhizosphere and phyllosphere bacterial communities, consistently enriching beneficial taxa, including <i>Pantoea ananatis</i> and members of <i>Acidobacteria</i>, while suppressing opportunistic groups. Concurrently, BY6 activated systemic defenses in poplar, evidenced by enhanced activities of key enzymes PAL and POD, and the upregulated expression of SA/JA pathway marker genes (<i>PR1</i>, <i>JAZ</i>, and <i>COI1</i>), coupled with the downregulation of the auxin transporter gene <i>AUX1</i>. These data indicate that the biocontrol efficacy of <i>B. velezensis</i> BY6 was mediated by a dual mechanism: the modulation of both rhizospheric and phyllospheric bacterial communities, direct elicitation of systemic defense pathways in poplar, which synergistically enhanced resistance against <i>A. solidipes</i>.