Soil microbial composition and vertical distribution patterns along the Liangshui River in Beijing, China

• Soil bacterial diversity and richness progressively decreased with increasing soil depth. • Soil bacterial and archaeal communities exhibited significant differences in composition across geological layers. • The dominant bacterial phyla in the soil were primarily Proteobacteria, Firmicutes, and Actinobacteria. • Povalibacter , Pedomicrobium , and Bauldia demonstrate as keystone taxa in Beijing’s urban soils. This study investigated the composition and vertical distribution of soil microbial communities in the vicinity of Liangshui River in Beijing. Soil samples (n = 18) were collected from depths of 0.1 m − 55 m, spanning three geological layers including artificial accumulation layer, recent sedimentary layer, and Quaternary sedimentary layer. These samples were analyzed using high-throughput sequencing to characterize bacterial and archaeal community composition. Results revealed that soil bacterial diversity and richness progressively decreased with increasing soil depth. Beta diversity analysis revealed that soil bacterial communities exhibited significant differences in composition across all three geological layers, whereas significant differences in soil archaeal communities were observed only between the artificial accumulation layer and the other two layers. At the taxonomic level, the dominant bacterial phyla in the soil were primarily Proteobacteria, Firmicutes, and Actinobacteria, with Bacillus being the predominant genus, while Crenarchaeota and Thermoplasmatota dominated the archaeal communities. PICRUSt2 functional prediction revealed that the soil bacterial communities were predominantly associated with carbohydrate metabolism, amino acid metabolism, and energy metabolism, among other functional pathways. Correlation network shows that Povalibacter , Pedomicrobium , and Bauldia may be keystone taxa in Beijing’s urban soils. This study not only elucidates the vertical distribution patterns of soil microbial communities along the Liangshui River, but also provides critical references for soil utilization and amendment strategies in Beijing.