Aims <p>Industrial emissions have increased acid deposition in the desert coal-mining regions of northwestern China. Empirical evidence indicates that acid deposition could impact ecosystem stability by altering microbial community. However, as these experiments fail to accurately replicate actual depositions, these impacts observed in high-intensity, short-period experiments may overestimate the long-term effects under real-world, gradual deposition conditions. Therefore, field studies focusing on major emission sources in these regions are needed to accurately assess the variations of microbial communities under ambient acid deposition.</p> Methods <p>This study investigated the composition and diversity of bacterial community through high-throughput sequencing technology, while examining how bulk deposition characteristics, plant characteristics, and soil properties influence bacterial community composition and diversity in the Ningdong Energy and Chemical Industry Base in northwest China.</p> Results <p>Ambient acid deposition shapes bacterial keystone taxa (Oxyphotobacteria) and diversity mainly through its effects on plant phosphorus (P) uptake and community diversity. Plant total P concentration affected the keystone taxa by altering soil organic carbon (C) and Shannon diversity regulated bacterial alpha diversity by altering soil particulate organic C. Ambient deposition had a positive effect on bacterial alpha diversity in moderate alkaline desert.</p> Conclusions <p>This study did not reveal a direct association between ambient deposition and keystone taxa. The main taxon and bacterial alpha diversity in the research region were changed as a result of plant total P concentration and species diversity impacted by exchangeable cation deposition. To elucidate delayed impacts of acid deposition on microbial keystone taxa, long-term monitoring and experiments are essential.</p>