Abstract
BACKGROUND : C. Fanjingshanensis is an extremely narrow-range species endemic to Mount Fanjing, the main peak of the Wuling Mountains in China. It has a highly restricted distribution and limited population size, grows primarily in mosses within alpine dwarf forests, and is highly sensitive to environmental changes, facing a high risk of extinction. Artificially assisted conservation is essential to maintaining its population. To ensure the success of future biodiversity conservation strategies such as ex situ conservation and habitat restoration, we used high-throughput sequencing to profile endophytes within C. fanjingshanensis tissues and microbial communities inhabiting its moss substrate and associated water layer. We analyzed the characteristics of both endophytic and habitat-associated microbiota and their relationships, providing a basis for optimizing microbial-assisted artificial habitat simulation. RESULTS: We identified 177 core bacterial and 37 core fungal genera in the moss layer, and 87 bacterial and 50 fungal genera in the moss water layer. More beneficial bacteria and pathogenic fungi were enriched in moss water, whereas the moss layer exhibited a more complex and positively associated microbial network. The endophytic bacteria belonged to 42 phyla and 1,198 genera, showing significant differences in dominant genera and community diversity among root, stem, leaf, and tuber. In contrast, endophytic fungi belonged to 16 phyla and 943 genera, but their diversity remained relatively stable across tissues. The dominant shared core endophytic bacterial and fungal genera were primarily derived from the dominant microbial genera in the moss water layer. CONCLUSION: There were substantial differences in habitat microbial community. More beneficial bacteria and pathogenic fungi were enriched in the moss water layer. The moss layer exhibited a well-structured, positively associated microbial community, which may facilitate resistance to environmental stress. Among tissues, tubers harbored significantly higher diversity and richness of endophytic bacteria compared to other tissues. Endophytic fungal diversity and community structure remained relatively stable. Moss water microbes were an important source of endophytes. This study provides a reference for the development of artificially assisted conservation strategies for alpine narrow-range species represented by C. fanjingshanensis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07046-z.