Multi-omics analysis of aroma differences in chili oil from different geographical origins using flavoromics and microbiomics

Chili peppers grown in different production regions often exhibit distinct aroma profiles. However, the soil–microbiome mechanisms underlying such origin-associated aroma variation remain poorly understood. Using a single cultivar and a fully standardized processing protocol, we compared two adjacent sites (PTG and ZJH) in Togtoh County with contrasting perceived chili oil aroma to elucidate the cascade from soil to fruit to oil. No climatic differences were found, yet soil N, P, S, and organic matter differed significantly and correlated with fruit traits (capsaicin, vitamin C, soluble solids, color). A consumer survey ( n = 117) provided exploratory evidence of perceived aroma: >86% perceived aroma differences, with PTG receiving 89% mention for “more aromatic”. Flavoromics clearly separated volatile profiles (R 2 Y = 0.987, Q 2 = 0.971; 200 permutation tests, P < 0.01), identifying 13 differential volatile markers, of which four (bornyl acetate, 6-undecanol, 5-methyl-2-furanmethanethiol, and (E,Z)-2,4-decadienal) showed relative odor activity values >1 and are candidate aroma-active compounds. These differential volatile markers were also associated with fruit quality traits. Microbiomics showed site-enriched bacterial taxa, enriched in Bacillus , Desulfitibacter , and Paenibacillus , with FAPROTAX-predicted enrichment of functions related to sulfur oxidation and lignin decomposition. Mantel analyses revealed a significant association between bacterial community structure and predicted functional profiles ( R = 0.667, P = 0.001). Procrustes analysis showed that both soil physicochemical properties (M 2 = 0.345, P = 0.001) and bacterial community composition (M 2 = 0.608 , P = 0.012) were significantly associated with the overall structure of fruit quality and aroma metabolites, with soil physicochemical properties showing a closer fit. Network analysis identified Desulfitibacter and Bacillus as potential hub taxa that were positively correlated with key differential volatiles ( P < 0.001), suggesting potential associations with aroma-related metabolic processes. Collectively, these results support an integrated association framework linking soil properties, microbial communities, fruit quality, and chili oil aroma differences, providing a basis for future targeted microecological regulation studies.