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• The microbial co-occurrence networks along soil depths in Mt. Oakley were analyzed. • There were contrasting patterns between soil bacterial and fungal diversity along altitudinal gradient. • Altitude was more important than soil depth for shaping soil microbial communities. • Main drivers of microbial community structure are consistent for whole and sub-network communities. • Sub-network community analysis revealed important drivers that do not capture by whole community. Soil bacterial and fungal communities with different key ecological functions play important roles in boreal forest ecosystems. Although several studies have reported on the altitudinal distribution patterns of microbes, our understanding of the characteristics of the microbial community and the core composition of the microbiome in cold-temperate montane forests is still limited. In this study, Illumina MiSeq sequencing was used to investigate the changes in soil bacterial and fungal communities in surface and subsurface soils along an altitudinal gradient (from 830 m to 1300 m) on Oakley Mountain. The diversity of the bacterial and fungal communities showed a monotonic decrease and a monotonic increase with altitude, respectively. The influence of altitude on the bacterial and fungal community composition was stronger than that of soil depth. The variations in pH and dissolved organic nitrogen content at different altitudes were the main factors influencing the bacterial and fungal community structures, respectively. There was no obvious difference between the network structures of the surface and subsurface soil fungal communities, while the network of the subsurface soil bacterial community was more complex and intricate than that of the surface soil bacterial community. The network nodes mainly belonging to Proteobacteria and Actinobacteria were the key bacterial taxa in the two soil layers. Although the main drivers of microbial community structure are consistent for whole and sub-nerwork communities, the subnetwork community analysis revealed other important drivers (i.e. soil temperature and nitrate nitrogen) that do not capture by whole community analysis. Thus, the more comprehensive picture of the important factors shaping microbial community structure can be achieved by combining whole and subnetwork community analyses. Our results demonstrated that altitude had a stronger influence on soil bacterial and fungal communities than soil depth and that bacterial and fungal communities showed divergent patterns with altitude and soil depth. [ABSTRACT FROM AUTHOR]