Raw data of potist in bulk soil

Soil protists are crucial mediators of biogeochemical cycles and ecological functions in agroecosystems. However, research on their ecological characteristics and functional roles under nitrogen management remains limited. Here, we elucidate the assembly mechanisms and ecosystem contributions of abundant versus rare protistan subcommunities across four major maize-producing regions under long term N fertilizationusing high throughput sequencing of 18S rRNA genes. Our results demonstrate that rare protists assemble via deterministic processes driven primarily by soil pH gradients, while abundant taxa follow stochastic mechanisms dominated by phosphorus availability. Within the rare subcommunity, predatory protists emerge as keystone regulators, exhibiting enhanced functional diversity and broader niche breadth. Crucially, rare protists maintained positive associations with soil multifunctionality through enhanced enzymatic activity and elemental cycling, contrasting with abundant taxa negative functional correlations. Alkaline soils buffered rare protists from N fertilization stress, amplifying their influence on community assembly. This work establishes a mechanistic framework linking agricultural management to protistan driven ecosystem processes, advocating for fertilization strategies that conserve functional diversity to enhance soil health