Microbial assembly and association network in watermelon rhizosphere after soil fumigation for Fusarium wilt control

Soil fumigation is an effective method to control soil-borne diseases like Fusarium wilt, however the processes and mechanisms driving microbial community reestablishment and pathogen suppression in the rhizosphere after fumigation remain poorly understood. In this study, we examined the dynamics of the rhizosphere microbiome and microbial network associations across different watermelon development stages and plant statuses (i.e. healthy and dead) after soil fumigation and organic fertilizer (OF) application in plastic shelters with Fusarium oxysporum f. sp. niveum (FON) heavily infected. Our results showed that fumigation treatments significantly reduced Fusarium wilt disease incidence and pathogen abundance, meanwhile, decreased soil microbial metabolic activity, fungal biomass and diversity. Bacterial community recovered from fumigation suppression in a short period, while fungal suppression was longer lasting, resulting in decreased fungi to actinomycetes (F/A) and fungi to bacteria (F/B) ratios in PLFA profiles. We further found some bacterial families, such as Actinospicaceae within Actinobacteria, Haliangiaceae, Rhizobiaceae and uncultured Rhodospirillales within Proteobacteria, Sporolactobacillaceae and Limnochordaceae within Firmicutes were greatly enriched after fumigation and might potentially contribute to pathogen suppression. The fumigation treatments significantly reduced microbial network complexity and the percentage of fungal nodes in comparison to un-fumigated control treatment. In contrast, a more complex microbial network was observed in the rhizosphere soil of healthy plants than that in the soil surrounding dead plant roots within fumigation treatments. Furthermore, healthy plant rhizosphere significantly enriched potential beneficial and nitrogen cycle-related bacterial phyla like Gemmatimonadetes, Verrucomicrobia, and Nitrospirae. More interestingly, Fusarium were markedly enriched in the rhizosphere soil of healthy plants and mainly represented by non-FON Fusarium like F. verticillioides and F. solani, implying a potential niche competition between FON and nonpathogenic Fusarium species in the rhizosphere of healthy watermelon. Taken together, our results provide vital information on the reconstruction of microbial communities and potential interactions between plant and its beneficial consortium after fumigation, which is instructive to develop more systematic strategies through targeting both beneficial and pathogen-similar taxa to improve disease control and soil suppression.