Low‐dose undecanone from Stenotrophomonas maltophilia suppresses Astragalus root rot and shapes the rhizosphere bacterial microbiome

Abstract BACKGROUND Astragalus membranaceus var. mongholicus is an important Chinese herbal medicine. Root rot in Astragalus caused by Fusarium oxysporum is a destructive soil‐borne disease. Biocontrol agents are currently regarded as an ecofriendly strategies for controlling root rot; however, the inherent complexity of natural environments often prevents beneficial bacteria from establishing long‐term residence in the plant rhizosphere. Therefore, more effective methods against pathogenic fungi are urgently needed to safeguard both the yield and quality of Astragalus , and harnessing microorganism‐derived volatile organic compounds (VOCs) is a promising strategy. RESULTS We isolated the bacterium Stenotrophomonas maltophilia strain B45 from the Astragalus rhizosphere that exhibited effective control of root rot. The ability of strain B45 to produce antibiotics and VOCs was determined to elucidate the possible mechanisms by which B45 inhibits pathogenic fungi. The results showed that the VOCs emitted by B45 significantly inhibited both mycelial growth and conidial germination in pathogenic fungi. Among the selected VOCs, 2‐undecanone demonstrated the strongest antifungal activity and caused severe structural damage to fungal cell walls. Pot experiments confirmed that 2‐undecanone fumigation markedly alleviated root rot symptoms in Astragalus . Furthermore, 2‐undecanone exhibited broad‐spectrum antimicrobial activity with a significantly strong inhibitory effect on both fungi and bacteria. This selective pressure led to substantial shifts in the rhizosphere microbiome composition of Astragalus . Notably, fumigation with low concentrations of 2‐undecanone increased the complexity of bacterial co‐occurrence networks and enriched beneficial genera, including Rhizobium , Bradyrhizobium , Sphingomonas and Lysobacter . CONCLUSION Our results indicate that low concentrations of 2‐undecanone did not compromise the disease‐suppressive capacity of the rhizosphere microbial community, and support the potential application of microbial VOCs as ecofriendly strategies for managing soil‐borne diseases in agriculture. © 2026 Society of Chemical Industry.