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

ABSTRACT Understanding the assembly mechanisms of soil microbial communities is critical for maintaining nitrogen cycling in agricultural ecosystems, which underpins soil fertility and sustains crop productivity. While environmental filtering and biotic interactions shape these communities, our understanding of how functional taxa interact with soil properties across extensive agricultural landscapes remains limited. Here, we investigated the influence of environmental factors on the Chinese agricultural soil microbiome, integrating assessments of microbiota diversity, composition, and assembly process. The results indicated that soil pH and moisture were among the strongest abiotic factors explaining the agricultural soil microbiota compositional variation at a continental scale, surpassing the examined geographical and climatic effects. Stochastic processes dominated the assembly of microbial communities in large-scale agricultural soils, whereas the relative importance of deterministic processes increased with rising pH from acidic to alkaline soils. Phylogenetic turnover, as indicated by the beta nearest taxon index (βNTI), revealed determinism peaked under nitrogen-limited conditions but weakened with moderate precipitation, suggesting that both extreme aridity and rainfall amplify environmental filtering. We also found that divergent environmental preferences were displayed by ammonia-oxidizing microorganisms, including four archaeal genera belonging to the Nitrososphaeria class. Their significant correlations with βNTI as well as soil pH, nitrate, and moisture suggested that soil properties likely influenced prokaryotic community assembly primarily through modulating these functional taxa. This study highlights the vital role of ammonia-oxidizing-related soil properties in shaping the functional groups and assembly mechanisms of soil microbial communities, while enhancing our understanding of how ecological niche modifications by ammonia-oxidizers influence community interactions and nutrient dynamics in agricultural soils. IMPORTANCE 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.