Variations in rhizosphere microbial community structure and function among diploid, triploid, and tetraploid watermelon cultivars

The rhizosphere microbiome, as the “second genome” of plants, plays a crucial role in nutrient acquisition, stress resistance, and soil health maintenance. Polyploidization is a key breeding strategy for watermelon: triploids are valued for seedlessness and high stress resistance, while tetraploids serve as important parental materials for triploid hybridization. However, how ploidy level (diploid, triploid, tetraploid) shapes the micro-ecological environment and microbial community assembly remains unclear. This study aims to investigate the associations between ploidy level and rhizosphere microbiota composition in watermelon. High-throughput sequencing (Illumina MiSeq PE300 for bacteria, PE250 for fungi) targeting the bacterial 16S rRNA gene and fungal ITS region was used to analyze rhizosphere microbial communities of diploid (HLL40-3), triploid (Guixi No.5), and tetraploid (MT410n-1) watermelons. α diversity, β diversity, taxonomic composition and functional prediction were performed to compare differences among groups. The Shannon index and richness indices (Ace and Chao1) of bacteria in the triploid were significantly higher than those in the diploid and tetraploid. Regarding fungi, only the richness in the triploid was significantly higher than that in the diploid and tetraploid. There was no significant difference in the fungal Shannon index between the triploid and diploid, and both were significantly higher than that of the tetraploid. β diversity analysis confirmed distinct separation of microbial communities across ploidy levels ( p < 0.05). Taxonomically, diploid rhizospheres were enriched in Proteobacteria , Melanconiella , and Hypomyces ; triploids were enriched in Bacteroidota , Microvirga , Mortierellomycota , Cercophora , and Neocosmospora ; tetraploids were specifically enriched in Patescibacteria , Gaiella , Trichoderma , and Papiliotrema . Functional prediction showed diploids were dominated by plant/wood saprotrophs; triploids harbored diverse functional guilds (animal pathogens, endophytes, soil saprotrophs, etc.); tetraploids had the highest relative abundance of undefined saprotrophs. Triploid watermelons establish a more diverse microbial community via selective recruitment, which might contribute to their superior agronomic characteristics.