Vegetation dominantly shapes the elevational patterns of archaeal and protistan communities and their ecological functions in the Hengduan Mountains, Tibetan Plateau

Abstract While elevational patterns of soil bacterial and fungal communities in mountain ecosystems have been well documented, the assembly processes of soil archaeal and protistan communities, and their linkage with ecosystem multifunctionality (EMF), remain poorly understood, particularly under the combined influence of vegetational, edaphic and climatic factors in the alpine forests of the Tibetan Plateau. To address this gap, an intensive quadrat survey along elevational gradients across three typical mountains in the south‐eastern Tibetan Plateau was conducted. Protistan and plant communities exhibited a consistent hump‐shaped alpha diversity pattern along the elevation, whereas archaeal diversity followed a ‘U’‐shaped pattern. Though climatic factors covaried with elevation, vegetation type emerged as the dominant driver, explaining the greatest variation in archaeal (22.51%) and protistan (19.74%) community assembly, followed by elevation‐dependent edaphic (16.17% and 12.63%) and climatic factors (10.28% and 11.35%). Stochastic processes dominated archaeal and protistan community assembly in mid‐elevation zones, while deterministic processes accounted for a higher proportion in low‐ and high‐elevation zones, in which harsh environmental conditions under the dry‐hot valley and timberline ecotones exerted stronger environmental selection pressures. Along the elevational gradient, archaeal dominance shifted from ammonia‐oxidizing Nitrososphaerales (>90% relative abundance) to non‐ammonia‐oxidizing Gagatemarchaeaceae (>80%), while photoautophic protists declined but parasitic protists increased, corresponding to vegetation succession from shrubland to broad‐leaved forest and then to coniferous forest. The soil EMF index, derived from soil and plant variables, was lowest under low‐elevation zones (Shrub) and peaked under sub‐alpine elevation zones (Fabri forest), aligning with trends in individual function category, that is soil nutrient cycling, microbial activity and plant performance. Notably, EMF correlated positively with archaeal ( R 2 = 0.67) and protistan ( R 2 = 0.69) beta diversity but not alpha diversity, underscoring the importance of specific microbial taxa in driving ecosystem functions. Overall, our study highlights the dominant role of vegetation in structuring archaeal and protistan communities in the alpine forest ecosystem of the south‐eastern Tibetan Plateau, and provides new insights into the distinct ecophysiology and ecological functions of archaea and protists. These findings offer valuable information for predicting below‐ground biodiversity responses to climate change and their feedback on ecosystem functions. Read the free Plain Language Summary for this article on the Journal blog.