Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected byFusarium oxysporumf. sp.lycopersici

Fusarium wilt of tomato caused by the pathogenFusarium oxysporumf. sp.lycopersici(Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated withFol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy andFol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration ofFolpathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors ofFolpathogen invasion.

Automated summary

The microbial community of healthy tomatoes is more stable and diverse compared to diseased tomatoes, potentially containing more potential suppressors of the Fusarium wilt pathogen. The study also found that microbial diversity is negatively correlated with the concentration of the Fusarium oxysporum f. sp. lycopersici pathogen.