Consecutive melon monocropping is associated with microbial community homogenization and reduced bacterial network complexity

Abstract

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 are widely used to alleviate the negative effects of monocropping, their long-term associations with microbial community structure and ecosystem functioning across monocropping durations remain insufficiently understood. Here, we collected 72 soil samples from Hami melon (Cucumis melo) fields at three sites in Turpan, northwestern China. All sampled fields received Bacillus subtilis–based bio-organic fertilizer and consisted of independently managed 1-year (M1), 3-year (M3), and 5-year (M5) monocropping systems sampled within the same year. Across fields with longer monocropping durations, key putative fungal pathogens, including Fusarium, Monosporascus, and Alternaria, showed lower relative abundances, whereas potentially beneficial bacterial taxa such as Bacillus, Paenibacillus, Sphingomonas, and Lysobacter were enriched. However, both bacterial and fungal communities exhibited reduced Bray–Curtis dissimilarity and β-dispersion, consistent with increasing microbial homogenization. Although the overall phylogenetic diversity of bacterial and fungal communities remained comparatively stable, the relative abundance and richness of rare taxa declined across monocropping durations. In addition, bacterial co-occurrence networks exhibited reduced complexity in fields with longer monocropping durations, while fungal subnetworks remained comparatively stable. Among the evaluated soil ecosystem functions, carbon degradation exhibited a non-linear response pattern and reached its highest value in M3, whereas nutrient cycling, carbon storage, and physical structure remained relatively stable across monocropping durations. Overall, our findings suggest that prolonged monocropping combined with long-term Bacillus subtilis–based bio-organic fertilization is associated with microbial community homogenization and simplified bacterial network structures, while most soil ecosystem functions remain comparatively stable.