In our study, we found that the endophytic bacteria community in healthy roots and clubroots were markedly different in alpha diversity and beta diversity. The domiant bacteria in healthy roots and clubroots were Proteobacteria at phylum level, while the relative abundance of proteobacteria were different. These results were in line with previous studies that many kinds of bacteria live in plant roots, including the phyla Proteobacteria, Actinobacteria and Bacteroidetes [19, 20]. In most studies, Proteobacteria are the predominant group of endophytic bacteria in various plant hosts [21, 22], suggesting they are suited to the ecological niche of plant tissue. Zhao also reported Proteobacteria as the dominant group of endophytic bacteria in the roots of oilseed rape (Brassica napus) . Actinobacteria was the second dominant groups in healty roots and had high relative abundance, which is in line with Zhao’s results . Some previous studies found that endophytic Actinomycetes had biocontrol capacity to inhibit some pathogens and also showed plant-growth-promotion traits [24–26]. In this study, Actinobacteria in healty roots maybe also play benefitial roles.
At the genus level, Pseudomonas dominanted in clubroots, suggesting that this bacteria play an important role in the ecological niche. They probably had advantage to tumorous stem mustard and maybe compete with P. brassicae for space and nutrition. Many previous studies verified that Pseudomonas possessed plant growth-promoting characteristics such as nitrogen-fixing , production of plant hormone or antimicrobial substances, or inducing systemic plant defense responses . The main bacteria in healthy roots was Rhodanobacter, which is also isolated from the roots of Spathiphyllum plants and has biocontrol activity against root rot fungal pathogen Fusarium solani [29, 30]. Rhizobium is widely distributed in plant root tissues and play a role in nitrogen fixation for plant hosts [31–33]. In healthy roots and clubroots, we observed abundant Rhizobium, indicating that the bacteria probably fix nitrogen for tumorous stem mustard.
It was reported that endophytic bacteria community was altered by pathogen infection in many plants species such as grapevine , apple  and tomato . Similarly, the differences in the endophytic bacteria community in healthy roots and clubroots were revealed by Hierarchical clustering analysis, PCA, NMDS and ANOSIM, suggesting that P. brassicae can restructure the endophytic bacteria community. To reveal how P. brassicae altered the community, we compared the physiological properties between healthy roots and clubroots and found that marked differences exist in SS, SP, M, SOD and POD, showing that P. brassicae infection significantly change the physiological characteristic. This is accordance with previous studies that soluble sugar distinctly increase under P. brassicae infection [35, 36]. In our study, soluble sugar had the most strongest correlation with the endophytic bacteria community in clubroot, suggesting that high concentration of soluble sugar change the community. In addition, soluble protein also increase in clubroots and correlated with the endophytic bacteria community. The high nutritional substances in clubroot induced by P. brassicae infection promote some endphytic bacteria proliferation, such as Pseudomonas, which possessed strong adaptation and ability of quick growth .
The methanol was also related to the endophytic bacteria community in clubroots. Previous studies showed that methanol production increased when plant cell wall endured mechanical wounding or other stresses such as pathogens or unsuitable temperature . P. brassicae infection leads to root cell swellling and damages cell walls, which may promote root cells releasing more methanol. The content of methanol in clubroots were markedly higher than healthy roots, which probably imparct on the endophytic bacteria community and promoted or inhibited some bacteria. For example, Duganella was the biomarker species in the community in clubroots, can utilize methanol as a carbon source . Abundant Duganella in clubroots may stimulated by methanol. The two-factor correlation network revealed that SS, SP and M were related to more endophytic bacteria, confirming SS, SP and M resturctured the endophytic bacteria community in clubroot.
SOD and POD are the antioxidase in plants and enhance plants stress tolerance to environment and pathogen. In general, POD and SOD increased when pathogen infected [40, 41]. However, SOD and POD in clubroots were lower than in healthy roots, reflecting that the normal physiological function maybe destroyed by P. brassicae infection. Moreover, the db-RDA demonstrated that SOD and POD positively and negatively correlated with the endophytic bacteria community in healthy roots and clubroots, verifing the fact that P. brassicae infection inhibited the activity of SOD and POD.