Impact of Bacterial Pustule Disease Occurrence on Bacterial and Fungal Communities Within Vegetable Soybean Plants

ABSTRACT Bacterial pustule of soybean caused by Xanthomonas citri pv. glycines is one of the most important foliar diseases that can affect the quality of vegetable soybeans. This study aimed to investigate the effects of natural bacterial pustule infection on the bacterial and fungal communities in the phyllosphere and rhizosphere of vegetable soybeans under field conditions using metagenomic sequencing of 16S rRNA and internal transcribed spacer (ITS) amplicons. The richness of the bacterial community was found to increase in leaves infected with X. citri pv. glycines . The occurrence of X. citri pv. glycines significantly impacted the beta diversity of both the bacterial and fungal communities in the phyllosphere but did not affect that in the rhizosphere. The composition of the bacterial and fungal communities differed between the field locations. The bacterial genera Xanthomonas , Pseudomonas and Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium , along with fungi in the family Didymellaceae and the genus Myrothecium , were significantly enriched in the infected leaves. In contrast, the abundances of the bacterial core microbiomes Methylobacterium , Aureimonas and Sphingomonas were significantly reduced in infected leaves. Co‐occurrence network analyses revealed that the diseased phyllosphere network had more intertwined interactions between bacterial and fungal genera than the healthy phyllosphere network, suggesting that bacterial pustules influence interkingdom interactions in the phyllosphere microbiome. This study provides insights into the interactions between X. citri pv. glycines and other plant‐associated microorganisms, as well as the associations of bacterial and fungal communities within the soybean– X. citri pv. glycines pathosystem.