Multi-omics analysis reveals associations among endophytic microbiome shifts, host transcriptional responses, and metabolic variation across variegated leaf sectors of Aspidistra elatior.

Leaf variegation in Aspidistra elatior provides a useful system for exploring localized plant-microbiome associations, yet the biological factors linked to sector-specific chlorosis remain unclear. To investigate potential relationships among endophytic microbial communities, host transcriptomic responses, and metabolic variation, we integrated 16S/ITS amplicon sequencing, transcriptomics, and widely targeted LC-MS/MS-based metabolomics across normal green (GG), adjacent green (SG), and chlorotic spot (SS) sectors. SS sectors showed sector-associated bacterial community patterns characterized by lower Shannon diversity relative to SG, enrichment of unclassified Rickettsiales, Stenotrophomonas, and Salinivibrio, and reduced abundance of several Actinobacteriota-associated taxa. By contrast, fungal community structure remained comparatively stable across sectors. Transcriptomic analysis identified sector-associated expression differences involving stress- and defense-related genes, including heat shock protein 70 (HSP70) and the F-box regulator SKIP23. Metabolomic profiling identified 52 core differentially accumulated metabolites (DEMs) between SS and SG, of which 37 showed higher abundance in SS. These metabolites included alkaloids, flavonoids, phenolic acids, and amino acids and derivatives. Integrated multi-omics correlation analyses linked host gene-expression modules to metabolite classes and revealed a significant correspondence between bacterial community dissimilarity and metabolic variation across sectors. Together, these findings identify SS sectors as spatially distinct leaf microenvironments in which bacterial community structure, host transcriptional state, and metabolite accumulation vary in parallel, placing localized variegation in a broader microbiome-host-metabolite context.