• Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils.
• Bacterial community in topsoils was influenced by both soil orders and soil forms, however, in subsoils it was more impacted by soil orders.
• Cropping increased the similarity of bacteria structures among different soil orders.
Human disturbances to soils can lead to dramatic changes in soil physical, chemical, and biological properties. The influence of agricultural activities on the bacterial community over different orders of soil and at depth is still not well understood. We used the concept of genoform and phenoform to investigate the vertical (down to 1 m depth) soil bacterial community structure in paired genosoils (undisturbed forests) and phenosoils (cultivated vineyards) in different soil orders. The study was conducted in the Hunter Valley area, New South Wales, Australia, where samples were collected from 3 different soil orders (Calcarosol, Chromosol, and Kurosol), and each soil order consists of a pair of genosoil and phenosoil. The bacterial community structure was analyzed using high-throughput sequencing of 16S rRNA. Results showed that bacterial-diversity decreased with depth in phenosoils, however, the trend is less obvious in genoform profiles. Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils. Thus, cropping not only affected topsoil bacteria community but also decreased its diversity in the subsoil. Bacterial community in topsoils was influenced by both soil orders and soil forms, however, in subsoils it was more impacted by soil orders. Constrained Analysis of Principal Coordinates revealed that cropping increased the similarity of bacterial structures of different soil orders. This study highlighted the strong influence of agricultural activities on soil microbial distribution with depth, which is controlled by soil orde