Distinct filtering processes shape bacterial and fungal communities and their co-occurrence patterns across garlic-associated compartments

BACKGROUND: Garlic (Allium sativum L.) is an important economic crop that is often subjected to continuous monoculture practices. Although the garlic rhizosphere is known to harbor growth‑promoting and disease‑suppressive potential, comprehensive investigations of microbial communities and interactions across the rhizosphere, roots, and leaves remain limited. In this study, bacterial and fungal communities in the rhizosphere soil, roots, and leaves of garlic plants grown under long-term monoculture in four major production regions of China were examined using amplicon sequencing, aiming to characterize the garlic‑associated microbiome and explore the potential pathogen‑antagonistic taxa under continuous monoculture. RESULTS: Microbial communities and their predicted functions were more strongly influenced by the compartment niche than by the production area, with distinct bacterial and fungal community patterns in each compartment niche. Source-tracking analysis revealed distinct colonization routes for bacterial and fungal communities in the garlic leaf endosphere. Bacterial communities in leaves appeared to be predominantly derived from the root endosphere, while fungal communities in leaves showed a potential direct derivation from the rhizosphere soil rather than roots. Potential pathogenic fungi were more abundant in rhizosphere soil and leaves than in roots. In the bacterial co-occurrence network, two modules abundant in roots and characterized by Pseudomonas and Flavobacterium were negatively associated with pathogen relative abundance. In the cross-kingdom network, keystone taxa included potential pathogenic ASVs from Verticillium and Fusarium, and they were negatively associated with bacterial taxa such as Lysinimonas and Microbacterium. CONCLUSIONS: These findings provide insights into the distinct colonization patterns of bacterial and fungal communities in garlic and their co-occurrence networks under long-term monoculture. The identification of bacterial taxa with antagonistic potential offers candidates for developing biocontrol agents to improve soil-borne disease management in garlic production.