Abstract Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β‐diversity along vertical (0–240 cm of soil depth) and horizontal spatial dimensions (~500,000 km2) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray‐Curtis) and phylogenetic (weighted Unifrac) β‐diversity. Additionally, we assessed whether the distance‐decay (horizontal dimension) was greater in the topsoil (0–30 cm) or subsoil (in each 30 cm layer from 30–240 cm) using Mantel tests. The influence of geographic distance versus edaphic variables on the bacterial communities from the different soil layers was also compared. Results indicated that the phylogenetic β‐diversity was impacted more by soil depth, while the taxonomic β‐diversity changed more between geographic locations. The distance‐decay was lower in the topsoil than in all subsoil layers analysed. Moreover, some subsoil layers were influenced more by geographic distance than any edaphic variable, including pH. Although different factors affected the topsoil and subsoil biogeography, niche‐based models explained the community assembly of all soil layers. This comprehensive study contributed to elucidating important aspects of soil bacterial biogeography including the major impact of soil depth on the phylogenetic β‐diversity, and the greater influence of geographic distance on subsoil than on topsoil bacterial communities in agroecosystems.
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