Chemotype-specific terpenoid divergence in Atractylodes lancea driven by host transcriptional profiles and endophytic microbiota: Functional validation of keystone strain ALX01

Atractylodes lancea consists of two distinct chemotypes, Dabie Mountain (DA) and Mao Mountain (MA), each with divergent terpenoid profiles. The mechanisms driving these differences remain unclear. This study utilizes transcriptomic, metagenomic, and gas chromatography–mass spectrometry (GC-MS) analyses of rhizomes from both chemotypes. Transcriptomics revealed significant upregulation of genes in the sesquiterpenoid pathway ( HMGS, DXR, and IDI ). Metagenomic analysis revealed chemotype-specific endophytic communities, with Pseudomonas spp. dominating DA rhizomes and Bacillus spp. prevailing in MA rhizomes. Metabolomics confirmed DA-specific accumulation of β-eudesmol (18.74 ± 1.82 mg/g) and hinesol (9.05 ± 0.93 mg/g), and an atractylone predominance in MA (22.36 ± 2.15 mg/g). A Mantel test established a robust correlation between Pseudomonas abundance and sesquiterpenoid levels ( r = 0.65, p = 0.013). Additionally, the screening of an endophyte repository comprising 224 DA isolates revealed that Pseudomonas sp. ALX01 increases DA-characteristic sesquiterpenoid production in axenic plantlets. Collectively, these results suggest that host transcriptional profiles and endophytic microbiota collaboratively influence chemotype development in A. lancea , supporting microbiome-based strategies for enhancing medicinal plant quality. • Multi-omics analysis uncovers the molecular mechanisms underlying chemotype divergence in Atractylodes lancea. • Inoculation with the endophyte Pseudomonas ALX01 enhances hinesol and β-eudesmol accumulation by 732 % and 281 %, respectively, in plantlets. • Sesquiterpenoid biosynthesis is co-regulated by host genes and the root microbiome. • The keystone strain ALX01 is sufficient to drive the formation of the Dabie Mountain chemotype under sterile co-culture conditions. • This study demonstrates that targeted microbiome engineering can effectively modulate terpenoid profiles in medicinal plants.