Optimisation of cropping and fertiliser management is essential to overcome the constraints of continuous cropping and to enhance crop yields. However, the combined effects of these practices on yield, through the regulation of soil fertility and microbial communities, remain unclear. To address this, a 13-year field experiment was conducted to assess the impacts of integrated management practices, including cropping systems (tobacco−fallow system, TFS; and tobacco–rapeseed system, TRS) and fertilisation treatments (no fertiliser, CK; moderate mineral fertiliser, NPK; and high mineral fertiliser, HNPK), on tobacco yield, soil fertility, and microbial communities. The results demonstrated that, across all fertilisation treatments, TRS increased the average yield by 46.1 % and soil fertility by 6.1 % compared to TFS. The cropping system was the primary factor shaping the overall microbial community structure (β-diversity), whereas fertilisation significantly influenced the relative abundance of specific microbial taxa (e.g., copiotrophs) within each system. TRS promoted fungal α-diversity and bacterial network complexity, whilst concomitantly suppressing pathogenic fungi. The mechanism underlying yield response to fertilisation varied with the cropping system. Under TFS, HNPK increased yield via a 'high-fertiliser nutrient compensation mechanism' by enhancing soil fertility. Specifically, HNPK increased soil fertility by 6.4 % and crop yield by 62.4 %, but it significantly reduced soil pH. In contrast, under TRS, NPK increased yield through 'soil–microbial synergy', which involved the simultaneous optimisation of soil fertility and enhancement of bacterial network complexity. Furthermore, bacterial network complexity was identified as the strongest predictor of yield. The TRS-NPK treatment outperformed TFS-HNPK in yield by 32.5 %, whilst avoiding soil acidification. This study underscores the critical role of soil bacterial network complexity in agricultural systems and demonstrates that combining crop diversification with moderate nutrient supply improves soil fertility, mitigates acidification, and enhances the sustainability of agricultural production.
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