Characterization of the root-associated microbiome provides insights into endemism of Thymus species growing in the Kazdagi National Park

Plant associated microbiomes have a large impact on the fitness of the plants in the particular environmental conditions. The root associated microbiomes are shaped by the interactions between the microbial community members, their plant host, and environmental factors. Hence, further understanding of the composition and functions of the plant root associated microbiomes can pave the way for the development of more effective conservation strategies for endangered endemic plants. Here, we characterized the bacterial and fungal microbiomes in bulk and rhizosphere soil of an endemic and a non-endemic Thymus species from Kazdagi National Park, Turkiye, Thymus pulvinatus and Thymus longicaulis subsp. chaubardii, respectively, by 16S rRNA gene and ITS amplicon sequencing. Our findings revealed no significant differences in alpha diversity between plant species and soil types. However, we found that the bacterial microbiome profiles differentiate not only Thymus species but also soil types while fungal microbiome profiles show distinct profiles particularly between the species in beta diversity. Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi members form the core bacterial microbiome while the fungal core microbiome consists of Ascomycota and Basidiomycota members in both Thymus species. Moreover, we identified the association of the bacterial taxa contributing to the biogeochemical cycles of carbon and nitrogen and providing the stress resistance with the rhizosphere soil of endemic T. pulvinatus. In addition, functional predictions suggested distinct enriched functions in rhizosphere soil samples of the two plant species. Also, employing an exploratory integrative analysis approach, we determined the plant species-specific nature of transkingdom interactions in two Thymus species.