Soil microbiome in long-term onion cropping systems

The soil microbiome is essential for ecosystem functions and food production; however, it undergoes structural and functional changes due to management practices. This study describes the microbial community associated with long-term onion systems: conventional tillage (CT), no-tillage (NT), and no-tillage vegetable system (NTVS). The long-term experiment was conducted over 17 years in Ituporanga, SC, Southern Brazil. The treatments included: CT (soil turned over before planting onions, followed by corn in summer and a fallow period in winter), NT (similar to CT but with restricted soil turnover), and NTVS (similar to NT but with greater species diversity grown in a consortium during summer, including millet + velvet-bean + sunflower). The soil microbiome (16S and ITS gene) was analyzed by next-generation sequencing - NGS of soil samples collected after the onion cycle. Soil management influenced microbiome structure, with each system exhibiting distinct compositional patterns. NTVS had a higher proportion of bacteria, fewer unclassified groups, and a greater abundance of taxa linked to nutrient cycling and beneficial plant relationships. NT showed a higher relative presence of archaea, particularly nitrifying groups such as Nitrososphaeraceae. In CT, Firmicutes and Bacillaceae were more prevalent, indicating a typical response to more disturbed environments. At all taxonomic levels, NTVS reduced the occurrence of unidentified taxa, suggesting a more stable environment with clearer ecological selection. For fungi, similar trends were observed, with higher richness in NTVS and lower in CT, favoring microorganisms adapted to stressful, fast-growing conditions and readily available nutrients. Both NT and NTVS showed increased abundance of microorganisms involved in nutrient cycling, organic matter decomposition, and symbiosis, which are vital for soil health. Therefore, conservation-oriented tillage systems, especially NTVS, foster a more diverse, functional, and potentially growth-promoting microbiome in the onion, whereas CT directs the community toward opportunistic and less functional groups.