Soil bacterial, fungal, and protistan assembly processes across a 1300 km climate and land-use transect

• Bacterial communities were primarily shaped by deterministic processes. • Fungi and protists, however, were more influenced by stochastic processes. • Land use in the humid area showed a stronger influence on microbial communities. • Soil pH plays the most important role in affecting the microbial assembly process. Soil microbial diversity is crucial to ecosystem functioning, yet it is increasingly threatened by the climate change and intensified land use. While microbial groups exhibit distinct environmental preferences, the specific mechanism driving their distribution patterns remains poorly understood. Here, we analyse microbial assembly processes using 16S, ITS, and 18S amplicon sequencing data from 141 soil samples. Our study spans a ∼1300 km transect across New South Wales, Australia, with a precipitation gradient from 229 mm (arid region) to 1338 mm (humid region) and three land uses (natural, pasture, and cropping). Our findings reveal that bacterial communities are predominantly shaped by deterministic processes, whereas fungi and protist communities are more influenced by stochastic processes. We also demonstrate that the assembly process significantly affects the microbial alpha and beta diversity. Climatic gradients affect microbial assembly, with bacteria showing distinct patterns compared to fungi and protists across the arid-to-humid climate. Land use further modulates these assembly processes within climate zones: in humid regions, it enhances variable selection for bacteria and ecological drift for protists, while in semi-arid regions, it promotes homogeneous selection for fungi. These insights into how climate and land management affect microbial assembly not only enrich our mechanistic understanding but also offer more reliable forecasts of soil ecosystem resilience in a changing world.