Effect of Powdery Mildew Pathogen Inoculation on Gene Expression Levels and Root Microbial Community Structures in Bottle Gourd and Pumpkin Seedlings

Bottle gourd and pumpkin are important rootstocks for producing grafted plants. However, the mechanisms by which the powdery mildew pathogen (Podosphaera xanthii) regulates bottle gourd- and pumpkin-related genes and metabolic pathways are not completely understood. In this study, the gene expression levels and microbial communities in the root soil of bottle gourd and pumpkin seedlings infected with powdery mildew were analyzed using Illumina sequencing. The total dry weight and stem weight of the pumpkin seedlings were considerably higher than those of the bottle gourd seedlings. The nitrogen content ranged from 688.79 mg kg^− 1 to 777.16 mg kg^− 1, the phosphorus content was between 110.64 and 267.67 mg kg^− 1 in the soils. The dominant bacterial species mainly included Proteobacteria, Acidobacteriota, Actinobacteriota, Bacteroidota, Gemmatimonadota, Chloroflexi, and the dominant fungal species included Ascomycota, Mucoromycota, Basidiomycota, and Chytridiomycota. Although the seedlings were infected with the same powdery mildew pathogen, the Kyoto Encyclopedia of Genes and Genomes functional groups differed extensively between bottle gourd and pumpkin. In the pumpkin seedlings, 623 genes were involved in the biosynthesis of secondary metabolites. In the bottle gourd seedlings, 39 and 65 genes were detected in the phospholipase and thyroid hormone signaling pathways, respectively. Powdery mildew affected nutrient absorption in the two types of seedlings and also greatly regulated the gene expression. The findings of this study are helpful for understanding the disease resistance mechanisms underlying sensitivity and non-sensitivity to powdery mildew pathogens in bottle gourd and pumpkin seedlings under greenhouse conditions.