Melon fruit microbiomes resemble aerial-tissue communities in a Turpan oasis field

Abstract Background Fruit-associated communities encounter belowground and aerial habitats, yet their position within the whole-plant microbiome remains unclear in field-grown melon. We profiled bacterial 16S rRNA gene and fungal internal transcribed spacer 1 (ITS1) amplicons from rhizosphere soil and surface-disinfected roots, stems, leaves and fruits. Four cultivars were sampled at fruit set and maturity in a randomised-block Turpan oasis field. Results Compartment was the strongest correlate of bacterial and fungal community structure. After nine melon-derived fungal operational taxonomic units (OTUs) were removed, the primary fungal analysis retained 805 OTUs across 152 samples. Compartment explained 28.6–46.8% of bacterial variation and 31.5–34.2% of fungal variation across Bray–Curtis and Aitchison distances; stage and compartment-by-stage terms were also supported. Primary whole-plot tests detected modest cultivar-associated variation under both distances, although the fungal Bray–Curtis result did not persist in the complete 120-sample sensitivity analysis, with a Benjamini–Hochberg-adjusted P value ( q ) of 0.167. Significant dispersion tests qualified several community-level effects. Fruit communities were closer to stems and leaves than to rhizosphere soil or roots. All four kingdom-by-distance fruit microbiome continuity scores exceeded their restricted null expectations, with one-sided P = q = 1/10,001. The dual-method screen identified 197 bacterial and 44 fungal stage-associated OTU-compartment associations. Seventeen bacterial OTUs met the abundance-occupancy criteria, whereas no fungal OTU met both thresholds. Whole-community composition was not significantly associated with the first principal component of fruit chemistry (PC1). Conclusions In this single-season field survey, melon fruit communities more closely resembled those of aerial tissues than those of belowground compartments. This pattern was consistent across kingdoms and distance measures, but it does not identify a source or route of microbial movement. The recurrent bacterial candidates and the absence of fungal OTUs meeting both recurrence thresholds provide focused targets for culture-based, localisation and strain-tracking experiments.