Ecological barrier of the Tianshan Mountains controls agroecosystem multifunctionality through soil microbial processes

Ecosystem multifunctionality (EMF) is influenced by rhizosphere microorganisms, and understanding how they regulate EMF has been an intriguing process to date. Here, amplicon sequencing was employed to investigate the diversity, assembly processes, and co-occurrence networks of rhizosphere bacteria and fungi in the topsoil (0–20 cm) across eight cotton ecosystems on both sides of the Tianshan Mountains in Xinjiang. Multifunctionality indicators were calculated based on soil properties and cotton attributes. The results indicated that rhizosphere microorganisms exhibited distinct clustering patterns between the northern and southern regions, where bacterial α-diversity was lower in the northern region than in the southern region, while this trend was reversed for fungi. Soil total potassium, carbon-to-nitrogen ratio, and urease activity primarily regulated bacterial diversity, while pH and electrical conductivity predominantly influenced fungal diversity. Deterministic and stochastic processes dominated bacterial and fungal community assembly, respectively; the proportions of dispersal limitation were larger in the southern region than in the northern region, while the proportions of homogeneous selection were reversed. The complexity and stability of microbial co-occurrence networks were higher in the southern region than in the northern region, with higher average degree (bacteria: north/south, 19.231/29.399; fungi: north/south, 4.969/24.585) and network density (bacteria: north/south, 0.015/0.020; fungi: north/south, 0.019/0.072), and lower modularity (bacteria: north/south, 0.700/0.669; fungi: north/south, 0.732/0.567). In addition, climatic conditions were the primary factors directly affecting multifunctionality indicators, and rhizosphere bacterial diversity influenced EMF by positively regulating SMF and cotton growth characteristics. Collectively, our findings carry important ecological implications for sustaining ecosystem service functions and elucidating the relationships between the functional diversity of rhizosphere microorganisms and EMF under multifaceted environmental interactions. © 2025 Elsevier B.V.