The removal of understory vegetation can rapidly alter the soil microbial community structure without altering the community assembly in a primary tropical forest

• Bacterial assembly was dominated by drift (stochastic processes). • Fungal assembly was more governed by heterogeneous selection (deterministic processes). • Understory removal rapidly altered fungal community structure. • Understory removal had minor effects on the community assembly of bacteria and fungi. There is little known about how understory vegetation affects the soil microbial community assembly, although it exerts strong controls on the soil microbial community composition. We attempted to clarify this question by establishing an experiment in which the understory vegetation was either removed or maintained as controls in a primary tropical forest in south China. The results showed that removing the understory markedly altered the structure of fungal rather than bacterial communities. The bacterial assembly in control sites was dominated by drift (stochasticity), whereas the fungal assembly was governed more by heterogeneous selection (determinism). Removal of the understory had minor effects on the community assembly of bacteria and fungi. These results indicate that the absence of understory vegetation in tropical forests can quickly alter the fungal community structure without influencing the community assembly.