Alpine plants occur at high elevation and sometimes above the tree line. They are well adapted to short growing seasons and low-nutrient soils. Plants utilize root exudates to provide source of nutrients for soil microbes and recruit some of them to the endosphere. In our previous findings, endophytic Pseudomonas species were predominant in alpine Miscanthus and Swertia in Hehuanshan mountain of Taiwan, suggesting a core microbiome may exist in the alpine plants in the same region. Here, we examined the microbial communities in endosphere with 16S metagenomic approach. Six alpine species from different phylogenetic lineages were collected at Hehuanshan Mountain in Taiwan in August 2018. They are Artemisia argyi (Asteraceae, Asterids), Ranunculus japonicus (Ranunculaceae, basal eudicots), Epilobium amurense (Onagraceae, Rosids), and Sedum morrisonense (Crassulaceae, sister to Rosids), all above belong to eudicots; Miscanthus sinensis var. transmorrisonensis (Poaceae, Commenlinids) and Ophiopogon japonicus (Asparagaceae, sister to Commenlinids), both of them belong to monocots. Higher species richness and diversity were found in monocots comparing to eudicots. Microbial community structure of monocot species are separated from eudicots, and Miscanthus samples displayed highest variation among all six species. Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were predominant among the six alpine plant species at class level. Monocot and eudicot species shared 92 core OTUs. Most of them are composed of Proteobacteria, Actinobacteria, and Firmicutes. Heatmap indicated that more diverse functions were enriched in monocot endosphere. Pseudomonas, Acinetobacter, Bradyrhizobium, Rhodoferax and Staphylococcus are common predominant endophytic genera to all six alpine plant species. Higher clustering and more interactions were found in the co-occurrence network of monocot than that of eudicot. In conclusion, endosphere microbiome highly dominated to monocot plant species and involved in the adaptation of all six plant species at alpine region.

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