Soil pH and nitrate shape deterministic assembly of microbial communities in agricultural soils via Nitrososphaeria

Agricultural soil microbiomes are essential for element cycling, fertility maintenance, and crop productivity, yet how key functional taxa interact with environmental factors to shape community assembly remains poorly understood. In this transcontinental study spanning diverse vegetation types, we demonstrate that ammonia-oxidizing archaea mediate soil microbial community assembly in response to pH and nitrate levels, with evidence of nonlinear threshold effects driven by nitrate. These findings underscore the pivotal role of keystone taxa in structuring soil biodiversity and ecological functions. Our study offers valuable insights into microbially mediated carbon and nitrogen cycling under climate change and supports crop-specific soil management strategies for sustainable agriculture.