Metabolomics-based comparison of metabolite profiles in Capparis spinosa L. from different habitats and associated soil factors

Introduction Capparis spinosa L. is a distinctive plant with edible and medicinal value, yet the factors influencing the accumulation of its effective components across diverse habitats remain unclear. This study aims to profile fruit metabolites and explore the association with rhizosphere soil environments. Methods Using LC-MS/MS-based untargeted metabolomics (six biological replicates per habitat), fruit metabolites from three habitats in northern Xinjiang (Urumqi, Karamay, and Ili) were profiled. Partial least squares discriminant analysis (PLS-DA) identified differential metabolites. 16S rRNA sequencing analyzed rhizosphere soil microbial communities, and correlation analyses linked fruit metabolites with soil metabolites and microbiota. Results A total of 1,739 metabolites were identified. PLS-DA revealed clear habitat separation, with 454, 340, and 411 differential metabolites in pairwise comparisons. Sixteen anti-inflammatory compounds (flavonoids, terpenoids, etc.) were candidate quality-associated metabolites, predominantly highest in Urumqi. Soil bacterial/fungal composition differed significantly among habitats, with Rubrobacterand Gaiella enriched in Urumqi. Correlation analysis linked 16 fruit metabolites (e.g., resveratrol, kaempferol) to 10 soil metabolites and specific soil genera. Discussion Habitat-driven differences in soil microbial communities and metabolite levels are associated with bioactive component abundance in C. spinosa fruit, offering targets for habitat selection and microbiome-informed cultivation. Note that LC-MS/MS signal intensities are semi-quantitative; reported differences reflect relative abundance rather than absolute content.