Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation

Abstract

Aims: Continuous cropping of watermelon is known to result in the disruption of the rhizospheric bacteria and fungi that contribute to the occurrence of Fusarium wilt disease. However, the underlying changes in microbial composition and function as a response to mono-cropping are less studied. Methods: In this study, differences in composition and potential function of the microbiome between healthy and diseased soils were investigated using MiSeq targeted sequencing and the functional GeoChip array, respectively. Results: Twenty years of continuous watermelon monoculture was found to significantly alter the soil microbial communities by increasing bacterial diversity but decreasing fungal diversity. Compare to bacterial network, fungal co-occurrence networks were less robust and less connected in the monoculture diseased soil. Identified keystone species, belonging to the Proteobacteria, Bacteroidetesand Acidobacteria, were present in both the diseased and healthy soils. Key fungal species from the healthy soil belonged solely within the Ascomycete, while in the diseased soil Basidiomycota were dominant. As such, overall variations in the composition of the soil microbiome are accompanied by changes in the identities of the keystone species when comparing healthy versus diseased soils, further suggesting that soil function may also be altered. Relative abundances of genes associated with the degradation of hemicelluloses and chitin, the Calvin circle, ammonification, stress responses, iron uptake, and nitrogen fixation were significantly higher under long-term monoculture. Particularly, Fusarium spp. relative abundance was positively correlated with the relative abundances of genes involved in adherence, cellular metabolism, and immune evasion which may facilitate pathogen infection of plant roots. Conclusions: In conclusion, these results highlight the significant compositional and functional differences in microbial communities between Fusarium wilt diseased soils and healthy soils under watermelon cultivation. This provides insight into the complex array of microorganisms in soils that suffer from Fusarium disease and illustrates potential directions towards the manipulation of the soil microbiome for suppression of this disease.