Phenolic acid biosynthesis is associated with deleterious microbiome changes during Plasmodiophora brassicae-induced clubroot in pakchoi.

Diverse diseases are typically associated with perturbed microbiome homeostasis, across ecosystems such as the gut and root habitats. Clubroot, which is caused by the devastating soil-borne pathogen Plasmodiophora brassicae, is a broad-spectrum disease that infects almost all cruciferous vegetables. However, the microbial ecological and metabolic cues underlying pathogen-driven deleterious disruptions of the microbiome remain enigmatic. In this study, changes in the microbiome and metabolome of the rhizosphere and roots in susceptible (diseased and nondiseased) and resistant pakchoi plants infected with P. brassicae were investigated. Diverse potential beneficial and disease-suppressive microbial families, including Rhizobiaceae and Sphingomonadaceae, were enriched in the healthy group compared with the diseased group. Rhizobiaceae was further characterized as a core driver family between the healthy and diseased groups. Reductionist-based strain validation studies further confirmed that Rhizobium sp. 25F3 showed drastic disease-suppressing activity in soil. The integrated metabolome‒microbiome correlation analysis revealed that phenolic acids were negatively correlated with the relative abundance of Rhizobiaceae. We further confirmed that genes related to phenolic acids were upregulated in diseased roots and that two phenolic acids suppressed beneficial Rhizobiaceae growth and accelerated P. brassicae infection in pakchoi. Upon P. brassicae infection, significant differences in the microbiome and metabolome were observed between diseased and healthy plants, as well as between resistant and susceptible varieties. Rhizobiaceae is dominant in the root microbiome and acts as a keystone family affected by P. brassicae infection. P. brassicae-induced phenolic acid metabolites selectively inhibit the growth of beneficial Rhizobium sp. 25F3 while promoting P. brassicae bursts in pakchoi. Our work provides ecological and metabolic explanations for how pathogenesis ultimately triggers a decrease in the relative abundance of beneficial microbes, which can guide future genetic and microbiome-based approaches to control clubroot disease. Video Abstract.