Rhizosphere Microbiome Characteristics of Grafted Watermelon and Own-Rooted Watermelon Under Continuous Cropping Soil Conditions

Abstract

Continuous cropping in tropical protected cultivation can impair soil health and increase the risk of soil-borne disease. We conducted a single-season field comparison in Hainan (October 2025–February 2026) to characterize the performance and rhizosphere microbial profiles of the mini-watermelon cultivar ‘Meiyue’ grown either on its own roots or grafted onto Cucurbita ficifolia. Plant growth, leaf gas exchange, fruit quality, and the field incidence of Fusarium wilt-like symptoms were recorded, and bacterial 16S V3-V4 and fungal ITS2 amplicons from the rhizosphere were sequenced. Grafted plants were taller and had thicker stems and longer internodes. Leaf chlorophyll content, stomatal conductance, and intercellular CO2 concentration were higher in grafted plants, whereas net photosynthetic rate did not differ between treatments. Wilt-like symptoms occurred in 55.41% of own-rooted plants, while no grafted plants developed symptoms during the trial. Mean single-fruit weight was 2.8-fold higher in the grafted treatment; grafted fruits were also larger and had a higher central soluble solids content. Bacterial and fungal beta diversity did not differ significantly between treatments (PERMANOVA, p = 0.100), although several taxa differed in relative abundance and LEfSe identified treatment-associated biomarkers. An exploratory functional-profile sensitivity analysis, performed after excluding one high-leverage own-rooted replicate, indicated modest differences in predicted nitrogen-transformation functions and fungal trophic modes; these predictions were not subjected to inferential testing. Correlations between microbial relative abundance and fruit traits were interpreted as associations rather than evidence of function. Within the constraints of a single-season, two-treatment study, watermelon grafted onto C. ficifolia showed better field performance and treatment-associated shifts in selected rhizosphere taxa under continuous-cropping conditions.