The plant rhizosphere acts as the first line of defense against the invasion of pathogens. The perturbation in the rhizosphere microbiome is directly related to plant health and disease development.

Root-rot disease caused by Fusarium oxysporum is a growing problem in agriculture for commercial cultivation of Panax notoginseng. Diverse microbes colonize plant roots, and numerous earlier studies have characterized the rhizospheric microbiome of P. notoginseng; nevertheless, the function of probiotic consortia on the rhizospheric microbiome against the root-rot disease remain elusive. We have compared and described the rhizospheric microbiome of lightly and severely diseased P. notoginseng as well as the interactions of the probiotic consortia and rhizospheric microbiome, and their function to alleviate the plant diseases were explored by inoculating probiotic consortia in bulk soil. From the perspective of microbial diversity, the rhizospheric dominant bacterial and fungal genera were utterly different between lightly and severely diseased plants. Through inoculating assembled probiotic consortia to diseased plant roots, we found that the application of probiotic consortia reshaped the rhizosphere microbiome, increasing the relative abundance of bacteria and fungi, while the relative abundance of potential pathogens was decreased significantly. We developed a microcosm system that provides a preliminary ecological framework for constructing an active probiotic community to reshape soil microbiota and restrain the disease. Microbial community structure differs between lightly and seriously diseased plants. The application of probiotic consortia changes the imbalance of micro-ecology to a state of relative health, reducing plant mortality. Plant disease suppression may be achieved by seeking and applying antagonistic microbes based on their direct inhibitory capability or by restructuring the soil microbiome structure and function.

Background: Bacterial wilt disease caused by the soilborne bacterium Ralstonia solanacearum is a serious threat to flue-cured tobacco production. In this study, an indigenous disease suppressive Bacillus strain was isolated from the rhizosphere soil of healthy tobacco plants, and its biocontrol and plant growth promoting (PGP) potential were evaluated in in-vivo and in-vitro assays. Results: Through isolation and screening of 250 isolates, WS-10 was found to be the best candidate antagonistic strain against R. solanacearum (WS-001). In-vitro assays revealed that the isolated strain WS-10 (Bacillus amyloliquefaciens) showed an effective antagonistic activity against R. solanacearum WS-001 and several plant-pathogenic fungi. As promising PGP rhizobacteria, WS-10 had the ability of nitrogen fixation, solubilization of inorganic potassium and phosphate, and biosynthesis of indole-3-acetic. In a co-culture assay, it significantly inhibits the growth of WS-001. Our greenhouse experiments showed that the soil physicochemical properties and accumulation of dry matter contents in different plant parts (roots, stems, and leaves) were significantly increased in the presence of B. amyloliquefaciens WS-10. The soil treated with B. amyloliquefaciens WS-10 displayed significantly higher values of the average well color development index, the utilization ability of 6 types of carbon sources by rhizosphere microorganisms, and the diversity indices of the rhizosphere microbial communities. In planta assay, B. amyloliquefaciens WS-10 significantly reduced tobacco bacterial wilt disease incidence by up to 73.36, 43.82, and 86.82% under three different treatments by improving the functional diversity and biological activity of the soil microbial community. Conclusions: Obtained findings suggested that B. amyloliquefaciens WS-10 had an excellent potential as a growth-promoting and biocontrol agent of tobacco bacterial wilt disease due to its multiple beneficial traits of nutrient solubilization and disease suppression. Thus, we conclude that B. amyloliquefaciens WS-10 was a high potential PGP and biocontrol strain for healthy production of tobacco crop.

Bacterial wilt caused byRalstonia solanacearumis a devastating disease of flue-cured tobacco production which poses significant yield losses all around the world. In this study, we evaluated the rhizosphere microbiome of healthy and bacterial wilt-infected (diseased) flue-cured tobacco plants through amplification of V3-V4 and ITS1-5f variable regions of 16S and internal transcribed spacer (ITS) rRNA. The study was based on the location (Qujing, Shilin, and Wenshan), plant components (rhizosphere soil and roots), and sample types (healthy and diseased) to assess the diversity of bacterial and fungal communities. Bacterial and fungal communities present in roots primarily emanated from rhizosphere soil. Healthy flue-cured tobacco plants exhibit high microbial diversity compared to diseased plants. Among three variables, plant components significantly influence the diversity of microbial communities, whereas rhizosphere soil harbors higher microbial diversity than roots. Bacterial phyla Cyanobacteria and Proteobacteria were found in high relative abundance in roots and rhizosphere soil samples, respectively. As far as fungi is concerned, a high relative abundance of Ascomycota and Basidiomycota was found in both rhizosphere soil and root. Bacterial genera such asBacillus,Bradyrhizobium,Ensifer,Neorhizobium, andLysobacterrelated to plant growth promotion and disease suppressing abilities were dominant than fungal genera. Analysis of relative abundance at specie-level revealed that most fungal species are pathogenic to flue-cured tobacco and could provide a conducive environment for wilt infection. In conclusion,R. solanacearumsignificantly influences the microbial diversity of flue-cured tobacco plants and negatively affects the bacterial community composition. Altogether, our study demonstrates the complexity of bacterial and fungal communities that possibly interact with each other (microbe–microbe) and host (host–microbe). This cross-talk could be helpful for healthy flue-cured tobacco plant growth and to induce resistance against bacterial wilt disease.

Clubroot disease, caused by Plasmodiophora brassicae, is a serious threat to Chinese cabbage (Brassica rapa subsp. pekinensis) production, which results in extensive yield losses. At present, clubroot control mainly depends upon pesticides, which provoke food-safety concerns, and the application of sole biocontrol agents cannot successfully control the disease. In this study, we investigated the effect of Bacillus cereus BT-23, Lysobacter antibioticus 13-6, and Lysobacter capsici ZST1-2 as sole strains, intra-/inter-genus co-culture, and microbial consortia on clubroot disease, plant growth, and rhizosphere bacterial diversity in a field experiment. The microbial consortia efficiently controlled the incidence of clubroot disease, with a biocontrol effect of about 65.78%, by decreasing the soil acidity and enhancing the yield (17,662.49 kg/acre). The high-throughput sequencing results demonstrated that the phyla Proteobacteria and Bacteroidetes were present in high relative abundance in the rhizosphere soil of the Chinese cabbage. Furthermore, Firmicutes was found as a unique phylum in the rhizosphere soil of CK-H and T1-T7, except for CK-D. The application of microbial consortia recovers the imbalance in indigenous microbial communities. Therefore, we conclude that microbial consortia can reduce the clubroot incidence in Chinese cabbage by decreasing the soil acidity and altering the diversity and structure of rhizosphere bacterial communities. This study highlights the potential of microbial consortia as an engineering tool to control devastating soilborne diseases in commercial crops.