Synergistic effects of grafting and companion cropping reshape the root endophytic microbiome network to regulate yield and fruit quality in continuously monocropped watermelon

Introduction Grafting and companion cropping alleviate continuous watermelon monocropping obstacles, yet their synergistic regulatory regulatory effects on root endophytic microbiota and fruit traits remain unclear. Methods A 2 × 5 split-plot field trial was conducted in a 7-year continuous watermelon monocropping system, comprising grafted and non-grafted plants with five companion cropping treatments designated CK, T1, T2, T3, and T4. High-throughput sequencing, PCoA, PERMANOVA, RDA, microbial co-occurrence network analysis and yield-quality assays were applied for systematic characterization. Results Grafting significantly increased total bacterial OTUs, all bacterial richness and diversity indices, fungal OTU numbers and fungal richness, yet reduced fungal community diversity. PERMANOVA verified that grafting, companion cropping and their interaction significantly reshaped bacterial and fungal community structures ( p < 0.001). Companion cropping reduced unique microbial OTUs and remodeled community composition and network topology. Under grafting conditions, companion cropping constructed tighter and more complex microbial networks and alleviated interspecies competition. LEfSe analysis demonstrated that grafting induced phylum-level differentiation of bacterial and fungal signature taxa, whereas companion cropping primarily modulated low-abundance and rare microbial assemblages. Grafting elevated yield titratable acidity and vitamin C while decreasing soluble sugar and soluble protein. Companion cropping raised soluble protein and vitamin C in grafted watermelon and improved yield, soluble sugar, soluble protein and vitamin C in non-grafted watermelon ( p < 0.05). All companion treatments significantly reduced titratable acidity (p < 0.05). RDA clearly separated grafted and non-grafted microbiota along the first axis and revealed directional correlations between dominant phyla and fruit traits, which were confirmed by Pearson correlation analysis. Discussion Combined grafting and companion cropping optimize watermelon yield and nutritional quality by restructuring the root endophytic microbial communities, offering a feasible cultivation strategy for sustainable continuous watermelon production.