Contrasting patterns and drivers of soil microbial communities in high-elevation montane grasslands and deserts of the Qinghai-Tibetan plateau in China

• Soil bacteria and eukaryotes have opposing α-diversity trends along an elevation gradient in alpine grasslands and deserts. • The soil bacteria–eukaryotic network is tighter and has more complex interactions in alpine grasslands than deserts. • Soil bacterial assembly in alpine grasslands and deserts is shaped by stochastic and deterministic processes. • Stochastic processes dominate the assembly of eukaryotes in alpine grasslands and deserts. Soil microorganisms are essential for ecosystem functioning, especially in an alpine/cold climate, yet their response along elevation gradients in different types of ecosystems within alpine cold regions is largely unknown. Here, we used Illumina MiSeq sequencing to investigate the geographic distribution, co-occurrence patterns, and assembly processes of topsoil (0–20 cm) microbial communities in alpine grasslands (3165–4903 m) and alpine deserts (3150–5200 m) of the east Qinghai-Tibetan plateau. Our results revealed contrary altitudinal distribution patterns for bacterial and eukaryotic α-diversity in the alpine topsoil of grasslands and deserts. Whether bacteria or eukaryotes, with rising elevation their α-diversity decreased linearly and significantly in alpine grasslands but instead increased linearly and significantly in alpine deserts. Soil bacterial community composition was strongly correlated with the soil pH of alpine grasslands, and with four ecological factors— EC (electrical conductivity) and pH in soil, MAP (mean annual precipitation), and MAT (mean annual temperature)—in the alpine deserts. Furthermore, although the soil eukaryotic community composition did not show a clear relationship to any ecological factors in alpine grasslands, it had a strong correlation with MAP in alpine deserts. Meanwhile, we detected a stronger more complex network structure of bacteria–eukaryota community interactions in alpine grasslands than in alpine deserts. Moreover, soil bacteria–eukaryota network complexity in alpine grasslands followed a unimodal pattern along the elevation gradient; however, for alpine deserts no elevation dependence was evident. Finally, our results confirmed that, whether in alpine grassland or desert, soil bacteria are governed by both stochastic and deterministic assembly processes. Unlike bacteria, however, stochastic processes (dispersal limitation and drift) mainly underpinned eukaryotic assembly in soil of both ecosystem types. Collectively, these findings advance our understanding of the geographic patterns and mechanisms driving the assembly of soil bacterial and eukaryotic communities in alpine ecosystems.