Endophytic microbiota and metabolites profile in gynoecious versus monoecious cucumbers

Sex expression in cucumber (Cucumis sativus L.) is a critical agronomic trait governing fruit yield and cultivation efficiency. Although its genetic and hormonal regulation is well-characterized, the role of endophytes and their metabolic interplay remains largely unexplored. In this study, an integrated approach, combining high-throughput sequencing of endophytic bacteria and fungi with untargeted metabolomics was conducted to investigate differences in endophytic community structure between gynoecious versus monoecious cucumbers. We found that gynoecious plants harbored bacterial communities with significantly higher richness, evenness, and a greater number of unique operational taxonomic units (OTUs) than monoecious plants, whereas fungal diversity was not significantly different. Although Proteobacteria, Actinobacteriota, and Firmicutes were dominant in both genotypes, gynoecious were uniquely enriched in Verrucomicrobiota and Myxococcota, while Patescibacteria characterized monoecious. LEfSe analysis identified Myxococcota and Bdellovibrionota as key biomarkers in gynoecious cucumbers, implying a potential for enhancing pathogen suppression. Functional prediction indicated that gynoecious-associated microbiota possessed stronger capacities for hydrocarbon degradation and iron respiration, whereas the microbiota-associated communities were enriched in pathways for nitrogen and nitrate respiration. Metabolomic analyses revealed pronounced genotype-dependent differences, including tryptophan metabolism, plant hormone signal transduction, linoleic and linolenic acid metabolism, and indole alkaloid biosynthesis were significantly upregulated in gynoecious root. Meanwhile, key metabolites, such as L-tryptophan, tryptamine, serotonin, indole-3-acetic acid, jasmonic acid, and salicylic acid were also accumulated at higher levels in gynoecious roots. Furthermore, correlation network analysis revealed stronger associations between specific microbial taxa and hormone- or defense-related metabolites in gynoecious plants compared to monoecious plants.