Continuous melon monoculture leads to microbial community homogenization and decreases bacterial network complexity

Background and aim Soil microbiomes are critical for sustaining ecosystem functioning and soil health. Monocropping often disrupts soil microbial communities, leading to yield penalties and soil degradation. Although bio-organic fertilizers may alleviate such negative effects, their impacts on microbial community composition and network structure under consecutive monocropping remain poorly understood. Methods Here, we collected 72 soil samples from Hami melon ( Cucumis melo ) fields at three sites in Turpan, northwestern China. All fields were continuously monocultured and soils were amended with Bacillus subtilis– based bio-organic fertilizer for 1, 3 and 5 years (designated M1, M3 and M5, respectively). Results With increasing monocropping duration, key putative pathogens and melon-specialist pathogens, including Fusarium , Monosporascus , and Alternaria , were suppressed, while beneficial bacteria such as Bacillus , Paenibacillus , Sphingomonas , and Lysobacter were enriched. However, within-treatment Bray–Curtis dissimilarity and β‑dispersion of both bacterial and fungal communities decreased, indicating progressive microbial homogenization. Consistently, the relative abundance and richness of rare taxa declined with increasing monocropping duration, while overall phylogenetic diversity of bacteria and fungi showed no significant change. The bacterial co-occurrence network displayed a gradual simplification, whereas the fungal network remained relatively stable. Among the assessed soil ecosystem functions, carbon degradation peaked at M3, while other soil functions remained unchanged. Conclusions Our findings indicate that melon monocropping drives microbial community homogenization, reduces the diversity and relative abundance of rare taxa, and simplifies bacterial network complexity. Under this management regime, bio-organic fertilizer effectively suppresses pathogen proliferation but has limited capacity to simultaneously enhance multiple soil functions.