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Ecological roles of "rare biosphere" (RB) were rarely discussed in alpine grassland ecosystems. We explored the roles of RB and specific taxa of soil bacteria and fungi in regulating soil nutrients and aboveground biomass of an alpine meadow and alpine steppe under warming and enhanced rainfall scenarios on the Qinghai-Tibetan plateau. In the context of alpine meadow and alpine steppe, the relative abundance of bacterial RB was 40% in the bacterial community, and it was <10% for fungal RB in the fungal community. The relative abundance of the RB of soil bacteria and fungi were not changed by warming or enhanced rainfall. All specific bacterial taxa and over 90% specific fungal taxa belonged to the RB. The RB, including the most specific taxa, explained many more variations in the contents of soil NO3-N and NH4-N than the high abundant microbial species under warming and enhanced rainfall conditions. The aboveground biomass of the alpine meadow and steppe were strongly affected by the contents of soil NO3-N, available phosphorus and total nitrogen under the condition of warming and enhanced rainfall. Our findings suggest that the robust soil microbial RB plays an important role in regulating the content of soil available nitrogen, which could profoundly affect aboveground plant biomass of alpine grassland ecosystems under climate change conditions.