Community structure of habitat microorganisms and endophytes of narrow-ranged species Corybas fanjingshanensis at different ecological niche specificities

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.

Keywords: Corybas; Core microorganism; Endophytes; Habitat microbes; Micro-niche; Orchid.

Fig. 1

Distribution of sampling points for C. fanjingshanensis. a Administrative District. b Mount Fanjing (The main peak of the Wuling Mountains). c Distribution of sampling point. d Habitat of C. fanjingshanensis. e C. fanjingshanensis plant

Fig. 2

Abundance of core bacteria and dominant bacterial genera: a Venn diagram of core bacterial genera in the moss layer. b Venn diagram of core bacteria in the moss water layer. c Venn diagram of shared core bacteria between the moss layer and the moss water layer. d Heatmap of the top 20 dominant bacterial genera by abundance in the moss layer and moss water layer. (M: different moss layers; W: different moss water layers; The numbers in the box represent the relative abundance of bacterial or fungal genera in different moss layers and moss water layers)

Fig. 3

Abundance of core fungi and dominant fungal genera: a Venn diagram of core fungi in the moss layer. b Venn diagram of core fungi in the moss water layer. c Venn diagram of shared core fungi between the moss layer and the moss water layer. d Heatmap of the top 20 dominant fungal genera by abundance in the moss layer and moss water layer. (M: different moss layers; W: different moss water layers; The numbers in the box represent the relative abundance of bacterial or fungal genera in different moss layers and moss water layers)

Fig. 4

LEfSe analysis of core microorganisms. a LEfSe analysis of core bacteria in the moss layer and moss water layer. b LEfSe analysis of core fungi in the moss layer and moss water layer. (M: different moss layer samples; W: different moss water layer samples)

Fig. 5

Microbial genus-level correlation network analysis. a Bacterial network in the moss layer. b Bacterial network in the moss water layer. c Fungal network in the moss layer. d Fungal network in the moss water layer. Each node corresponds to a bacterial or fungal genus, while the edges denote significant correlations (Spearman’s r > 0.6, p < 0.05) between them. Red edges represent positive correlations, whereas green edges indicate negative ones

Fig. 6

The abundance of endophytic microbial communities in 4 tissues of C. fanjingshanensis at various classification levels. a Unique and shared ASVs of endophytic bacteria. b Unique and shared ASVs of endophytic fungi. c Major species composition of endophytic bacteria at the genus level. d Major species composition of endophytic fungi at the genus level. (T: tuber; L: leaf; R: root; S: stem)

Fig. 7

Alpha diversity and PCoA analysis of roots, stems, leaves, and tubers. a Alpha diversity analysis of endophytic bacteria. b Alpha diversity analysis of endophytic fungi. c PCoA analysis of endophytic bacteria. d PCoA analysis of endophytic fungi. (T: tuber; L: leaf; R: root; S: stem; *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001)

Fig. 8

Abundance of shared core microorganisms and functional composition of endophytic fungi of C. fanjingshanensis. a Abundance of shared core bacteria in the moss layer and moss water layer. b FUNGuild analysis of endophytic fungi in root, stem, leaf, and tuber. c Abundance of shared core fungi in the moss layer and moss water layer. (M: Moss layer; W: Moss water layer; T: Tuber; L: Leaf; R: Root; S: Stem)

Fig. 9

Distribution of KEGG second-level functional gene abundances of endophytic bacteria in the tubers, leaves, roots, and stems of C. fanjingshanensis