Continuous cropping drives assembly process of soil microbial community to alter keystone taxa causing challenges

Background Continuous cropping obstacles pose a serious threat to sustainable agricultural development, making it crucial to understand the microbial mechanisms underlying these challenges. Methods In this study, tobacco was subjected to different planting durations: 1 year (CR), 5 years (CC5), 10 years (CC10), and 15 years (CC15). The rhizhosphere microbial community assembly process, composition, keystone taxa, and their relationship to continuous cropping challenges were analyzed. Results The rhizosphere bacterial community in CC5 was predominantly shaped by deterministic assembly processes, distinguishing its community structure from those of the other treatments. Co-occurrence network analysis revealed that the number of nodes and edges involved in bacterial-fungal interactions decreased by 22.70% and 79.86%, respectively, in CC5 compared with CR. This decrease was accompanied by a reduction in the abundance of beneficial microbes (Rhodanobacter, Ellin6067, Frankiales, and Setophoma) and an increase in harmful microbes, such as Verticillium, exacerbating continuous cropping challenges. In CC10, bacterial community assembly was primarily dominated by stochastic processes. Although the number of network nodes and edges increased by 21.96% and 204.73%, respectively, compared with CC5, they remained lower than those in CR. By extending the continuous cropping to 15 years, the bacterial community assembly was shaped by stochastic processes. Compared with CC5, the number of network nodes and edges increased by 34.39% and 405.44%, respectively. Additionally, the abundance of beneficial microbes increased, while harmful microbes such as Verticillium decreased, resembling the levels observed in CR. Conclusions Overall, the bacterial community in CC5 was driven by deterministic assembly processes, resulting in a distinct structure. The complexity and stability of the co-occurrence network significantly decreased, accompanied by a higher abundance of harmful microbes and a lower abundance of beneficial microbes, which exacerbated the continuous cropping obstacles. In contrast, after 15 years of continuous cropping, the bacterial community assembly shifted to stochastic processes, which strengthened the co-occurrence network complexity and stability, increased beneficial microbes, and alleviated continuous cropping challenges.