Bio-Organic Fertilizers Enhance Yield in Continuous Cotton Cropping Systems Through Rhizosphere Microbiota Modulation and Soil Nutrient Improvement

The application of bio-organic fertilizers (BOFs) represents a promising strategy for mitigating soil degradation in continuous monoculture systems, yet their long-term mechanistic impacts in aged cotton fields remain poorly elucidated. This study aims to uncover how BOFs enhance soil health, reshape microbial communities, and sustain cotton productivity under decades-long continuous cropping in Xinjiang, China. A two-year field experiment compared conventional chemical fertilization (CK, N−P−K: 300–180–150 kg·ha⁻¹) with combined chemical and BOF treatment (BOF, N−P−K: 300−180−150 kg·ha⁻¹, BOFs: 4159 kg·ha⁻¹ in 2023 and 4545 kg·ha⁻¹ in 2024). The BOFs used in this study contained ≥40.0% organic matter and ≥0.20 × 10⁸ CFU·g⁻¹ of <i>Bacillus amyloliquefaciens</i>. The results demonstrated that BOF application significantly increased seed cotton yield by 19.82–28.17% and total plant biomass by 56.66–61.97%, with the latter reflecting improved root development and nutrient acquisition—key factors contributing to yield gains. Soil analysis indicated substantial elevations in organic matter (12.05–17.72%) and available nutrients without altering pH. Metagenomic sequencing revealed that the BOF treatment enriched beneficial taxa (e.g., <i>Lysobacter</i> increased by 50.53%), suppressed <i>Fusarium</i> (decreased by 36.08%), enhanced microbial network complexity, and reinforced disease-suppressive functions. These findings provide mechanistic insights into the role of BOFs in restoring rhizosphere ecology and promoting soil resilience. This study supports the practical integration of BOFs as a sustainable measure for rejuvenating degraded cotton monoculture systems and optimizing fertilizer management in arid agroecosystems.