Comparative microbial community analysis of Oreocharis mileensis

Plants dynamically interact with their microbiomes through phytohormonal signaling and defense responses, shaping microbial diversity and ecosystem function. While resurrection plants host growth-promoting microbes, prior studies on different resurrection plants have been limited to localized sampling, potentially underestimating microbial diversity. We analyzed bacterial and fungal communities across five Oreocharis mileensis populations, a potential ornamental resurrection plant, to determine: population-level microbiome differences or affinity, potential microorganisms that help during desiccation of the plant and their conservation across populations. We found that microbial composition was strongly influenced by compartment (bulk soil, rhizosphere, endosphere) but exhibited only moderate drought-induced changes, suggesting O. mileensis maintains a stable microbiome under stress. Core phyla (e.g., Proteobacteria, Actinobacteriota, Ascomycota) were conserved across populations, but genus-level core taxa relatively varied, reflecting niche specialization. Drought increased alpha diversity while reducing beta diversity in bacteria, indicating homogenization driven by stress-tolerant taxa like Actinobacteriota. Fungal responses differed, with increased beta diversity suggesting drought-enhanced compositional turnover. Key bacterial genera (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Rhizobium) dominated hydrated states, while drought enriched Actinobacteria (Microlunatus, Rubrobacter) or other drought resistant taxa. Fungal communities shifted from saprotroph-dominated hydrated states to symbiotic taxa (e.g., Paraboeremia, Helotiales) under drought. Functional profiling revealed compartment-specific metabolic specialization, with drought enriching stress-response pathways (e.g., secondary metabolite biosynthesis, signal transduction). These findings demonstrate that O. mileensis microbiomes are structured by compartmental filtering and exhibit drought-driven functional plasticity, with conserved stress-adapted taxa potentially supporting host resilience. This study expands our understanding of microbiome assembly in resurrection plants and highlights candidates for microbiome engineering to enhance crop stress tolerance.