Biochar-based microbial fertilizer enhances cucumber growth and yield by improving soil quality in protected agriculture

Intensive protected agriculture is highly productive, but its sustainability is increasingly constrained by soil degradation. To explore effective green soil strategies, this study evaluated the effects of Bacillus subtilis (BS), biochar (BC), and their composite biochar-based microbial fertilizer (MF) applied at four rates on soil physicochemical and biological properties, as well as crop growth and yield. A data-driven Soil Quality Index (SQI) framework integrating K-means clustering, principal component analysis (PCA), and canonical correlation analysis (CCA) was developed to quantify soil quality. Furthermore, partial least squares structural equation modeling (PLS-SEM) was employed to elucidate the multi-pathway response mechanisms of the soil–crop system. The results showed that MF treatment outperformed individual BS and BC treatments in improving soil structure, nutrient availability, and microbial activity. Compared with the control (CK), MF reduced soil bulk density by 10.8% and increased field capacity by 19.0%. It also increased available phosphorus and urease activity by 28.9% and 29.1%, respectively, and significantly improved microbial diversity, as evidenced by higher Shannon and Chao1 indices. The MF achieved the highest SQI (0.79), representing a 46.3% improvement over the CK, and increased cucumber yield by 24.23% at an application rate of 1.0% (w/w). Moreover, PLS-SEM further revealed that MF enhanced soil quality and crop yield primarily through three synergistic pathways: strengthening water-nitrogen coupling, activating phosphorus and potassium pools, and stimulating organic matter turnover and enzyme activity. Overall, this study demonstrated that MF substantially improved soil quality and cucumber yield through multi-dimensional synergistic mechanisms. The proposed data-driven SQI framework provided a robust and comprehensive approach for quantifying soil quality dynamics, offering both a theoretical basis and practical guidance for sustainable soil management in intensive agricultural systems. • Biochar-based microbial fertilizer shows strong synergy in improving soil quality. • Data-driven SQI framework objectively evaluates comprehensive soil improvement. • The fertilizer increases cucumber yield by 24.23% under protected cultivation. • Higher cucumber yield is driven by better water, nutrient, and microbial balance.