Comparative multi-omics of host genome, metabolome and associated rhizosphere microbiota across karst-endemic and widespread Rhododendron species

Abstract Background To examine how classically calcifuge plants persist in phosphorus-poor, high-Ca 2+ karst bare-rock habitats, we compared genome, leaf-metabolome and associated rhizosphere-microbiome patterns in the karst-endemic Rhododendron bailiense Y.P.Ma, C.Q.Zhang & D.F.Chamb. with those in the widespread R. delavayi Franch. and allopatric R. ambiguum Hemsl. We integrated a multi-omics investigation across three natural microhabitats to decode these inter-kingdom interactions, combining whole-genome comparative analysis, UHPLC-MS/MS non-targeted leaf metabolomics, fungal internal transcribed spacer (ITS) amplicon profiling, and deep rhizosphere metagenomic sequencing. Results Comparative genomics revealed significant expansion of secondary metabolism gene families in R. bailiense . Metabolomics showed a distinct chemical profile rich in specific flavonoids and polyacetylenes, such as luteolinidin and safynol. These species-specific metabolite profiles co-varied with microbial hubs, including Piloderma , Streptomyces , Pseudorhodoplanes and Candidatus Sulfotelmatobacter , whose reported or predicted functions are relevant to phosphorus mobilization, rhizosphere defence, recalcitrant-carbon turnover and mineral-associated sulfur cycling. In contrast, the R. delavayi and R. ambiguum rhizospheres were enriched in saprotrophic taxa, including Mortierella , consistent with broader nutrient-turnover potential. Conclusions R. bailiense showed a species-specific leaf-metabolite profile that co-varied with a distinctive rhizosphere microbiome. Together, these coordinated patterns suggest a potential functional link between species-specific host chemistry and rhizosphere-community organization, and highlight microbial and metabolic candidates relevant to karst persistence and conservation.