Critical endophytes in fruit associated with volatile profiles in domestic Xinjiang melons

Melon ( Cucumis melo L.) is renowned for its high nutritional value and distinctive aroma profile, with Xinjiang being one of the primary production regions. However, the aroma characteristics of Xinjiang melons and their associations with fruit-associated microbiomes remain insufficiently understood. To investigate the factors contributing to these aroma characteristics and identify critical endophytes in fruit, the soluble solids content (SSC), titratable acid (TA), total sugar content (TSC), vitamin C (VC), volatile organic compounds (VOCs) and microbial communities of Flavor No.4 (F4), Flavor No.8 (F8), Yellow 9818 (Y9818), and Green 9818 (G9818) were determined using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC–MS) and high-throughput sequencing (HTS) techniques. A total of 84 VOCs were identified, with alcohols representing a relatively high proportion (2.20%∼20.16%) and esters showing a wide compositional diversity (1.49%∼8.36%). Additionally, 8 VOCs with potential aroma activity contributed to the green, fruity, and floral aromas of Xinjiang melons. G9818 may be more accessible to consumers because of its optimal solids-to-acidity ratio, exceptional VC, and distinctive aroma profiles. Microbial analysis revealed differences among tissue compartments and cultivars, with endophytic fungi exhibiting stronger variety-related variability than endophytic bacteria. Multivariate analysis identified 15 candidate critical endophytes showing 56 strong associations with 40 VOCs. Pseudeurotium, Acremonium, Fusarium, Neocosmospora , and Naganishia were identified as hub genera. These findings provide reference indicators for flavor quality evaluation and microbial resource screening in Xinjiang melon production.