Host genotype and edaphic factors shaped bacterial communities associated with native and endemic medicinal Artemisia species in arid environment

BACKGROUND: Plant-associated microbiomes are key contributors to plant nutrition and stress tolerance, particularly in arid ecosystems where extreme abiotic conditions strongly shape plant-microbe interactions. Despite this, the abiotic drivers of microbiome assembly across different plant compartments in wild medicinal species from these environments remain poorly understood. In this study, we investigated bacterial community structure across multiple niches, including bulk soil, rhizosphere, root, and shoot, in three wild Artemisia species (Artemisia herba-alba Asso., Artemisia negrei L., and Artemisia mesatlantica Maire), the latter two being endemic to arid regions of Morocco. RESULTS: Using amplicon sequencing, we observed diverse bacterial associations with each plant niche harboring distinct taxa. Host plant species significantly influenced bacteriome composition (p = 0.026), particularly in Artemisia mesatlantica, which hosted the most specific bacterial taxa compared to its other relatives. Plant compartment emerged as key drivers of belowground bacterial community assembly with additional structuring by host species and edaphic factors. Soil pH, calcium carbonate content, organic matter and electrical conductivity were strongly correlated with shifts in bacterial diversity and composition, emphasizing the role of soil physicochemical properties as an environmental filter under extreme alkaline and arid conditions. Despite these species- and environment-specific variations, a conserved core bacteriome was identified across all Artemisia species, and compartments except shoot, comprising of Bacillus, Microvirga and Rhizobium. CONCLUSION: Our results demonstrate that the interplay between host identity and soil properties orchestrates distinct, yet functionally coherent bacterial communities in wild Artemisia species. Bacterial taxa identified as core are well-known for their roles in plant growth promotion, biocontrol and production of bioactive secondary metabolites. The persistence of this core bacterium comprising of Bacillus, Microvirga and Rhizobium suggests a stable association across hosts and compartments, potentially reflecting conserved ecological roles, although functional contributions were not directly assessed in this study. Overall, our findings reveal how the interplay between soil properties and host identity shapes the assembly of distinct, yet compositionally consistent bacterial communities in wild medicinal Artemisia species.