Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage’s resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.

Sclerotium rolfsii causes destructive soilborne disease in numerous plant species, and biological control may be a promising and sustainable approach for suppressing this widespread pathogen. In this study, the antagonistic effect against S. rolfsii of 10 Trichoderma strains was tested by the dual culture method, and a gliotoxin-producing strain, T. virens T23, was shown to be the most effective, inhibiting growth of S. rolfsii in vitro by 70.2%. To clarify the antagonistic mechanism and gliotoxin biosynthesis regulation of T23, a gliotoxin-deficient mutant was constructed via Agrobacterium tumefaciens-mediated gene knockout in vivo. As expected, disruption of the gene located in the putative gliotoxin biosynthesis gene cluster, gliI-T, resulted in gliotoxin deficiency and attenuation of the antagonistic effect against S. rolfsii, indicating that gliotoxin biosynthesis is regulated by gliI-T and that gliotoxin is an important antifungal metabolite of T23. Transmission electron microscopy revealed that gliotoxin treatment caused marked alterations of the hyphal cells of S. rolfsii depending on the drug concentration, whereby one of the prominent structural alterations was a reduction in the number and length of mitochondrial cristae. When S. rolfsii was exposed to 30 μg/ml of gliotoxin for 12 h, striking plasmolysis and ultrastructural changes were induced. The results demonstrated that gliotoxin is an important secondary metabolite of T. virens T23 in its antagonism against S. rolfsii.

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.

The productivity and quality of agricultural crops worldwide are adversely affected by disease outbreaks and inadequate nutrient availability. Of particular concern is the potential increase in mycotoxin prevalence due to crop diseases, which poses a threat to food security. Microorganisms with multiple functions have been favored in sustainable agriculture to address such challenges. Aspergillus flavus is a prevalent aflatoxin B₁ (AFB₁)-producing fungus in China. Therefore, we wanted to obtain an anti-aflatoxigenic bacterium with potent mycotoxin detoxification ability and other beneficial properties. In the present study, we have isolated an anti-aflatoxigenic strain, BC11-1, of Burkholderia contaminans, from a forest rhizosphere soil sample obtained in Luzhou, Sichuan Province, China. We found that it possesses several beneficial properties, as follows: (1) a broad spectrum of antifungal activity but compatibility with Trichoderma species, which are themselves used as biocontrol agents, making it possible to use in a biocontrol mixture or individually with other biocontrol agents in an integrated management approach; (2) an exhibited mycotoxin detoxification capacity with a degradation ratio of 90% for aflatoxin B₁ and 78% for zearalenone, suggesting its potential for remedial application; and (3) a high ability to solubilize phosphorus and produce cytokinin production, highlighting its potential as a biofertilizer. Overall, the diverse properties of BC11-1 render it a beneficial bacterium with excellent potential for use in plant disease protection and mycotoxin prevention and as a biofertilizer. Lastly, a pan-genomic analysis suggests that BC11-1 may possess other undiscovered biological properties, prompting further exploration of the properties of this unique strain of B. contaminans. These findings highlight the potential of using the anti-aflatoxigenic strain BC11-1 to enhance disease protection and improve soil fertility, thus contributing to food security. Given its multiple beneficial properties, BC11-1 represents a valuable microbial resource as a biocontrol agent and biofertilizer.

Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant’s ‘second genome’, plays a pivotal role in maintaining plant health and defending against pathogen invasion. Recent advances in multi-omics technologies, synthetic microbial communities (SynComs) construction, and rhizosphere metabolomics have significantly advanced our understanding of the mechanisms by which rhizosphere microbiomes suppress soil-borne diseases. This review systematically summarizes the following: 1. key drivers of rhizosphere microbial community assembly, particularly plant “cry for help” signaling; 2. core beneficial microbial taxa and their disease-suppressive mechanisms; 3. the critical role of microbial interaction networks; 4. microbiome-based management strategies and their application progress; and 5. current challenges and future research directions. Compared with previous reviews that separately discussed rhizosphere microbiota, disease-suppressive soils, synthetic microbial communities (SynComs), or prebiotics, this review uniquely integrates multiple levels of regulation, from plant genetic determinants (‘M genes’) and root exudate-mediated ‘crying for help’ to microbiome engineering (SynComs and prebiotics) and cross-kingdom interactions (bacteria–fungi–protists–phages). A central conceptual axis of ‘M genes → microbiome engineering → breeding’ is proposed, bridging plant genetics, microbial ecology, and crop improvement for durable disease suppression. Ultimately, this work aims to provide a theoretical foundation for developing efficient and sustainable green control technologies against soil-borne diseases.

Southern blight caused by Sclerotium rolfsii is a devastating soil-borne disease of Aconitum carmichaelii, a medicinal plant widely cultivated in China. Biological control using beneficial bacteria offers a sustainable alternative to chemical fungicides. This study investigated the influence of Bacillus subtilis FZ-7 on rhizosphere microbiome assembly and disease suppression in A. carmichaelii under field conditions. Four treatments were established: uninoculated control (C group), single inoculation with B. subtilis (B group), single inoculation with S. rolfsii (S group), and co-inoculation of S. rolfsii and B. subtilis (BS group). Plant biomass, soil physicochemical properties, and rhizosphere bacterial and fungal communities were analyzed using high-throughput sequencing of 16S rRNA and ITS genes, along with co-occurrence network analysis. Results showed that B. subtilis inoculation suppressed this growth suppression. B. subtilis alone enhanced both bacterial and fungal diversity. PCoA and LEfSe analyses revealed distinct microbial community structures among treatments, with biomarkers such as Lactobacillus, Candidatus Nitrosotalea, Rhodanobacter, and Sphingomonas for bacteria, and Trichocladium, Conocybe, Plectosphaerella, and Athelia for fungi. Co-occurrence network analysis indicated that co-inoculation of S. rolfsii and B. subtilis partially restored cooperative microbial associations. Soil organic matter, pH, and cation exchange capacity were the main environmental factors shaping microbial community composition. Shoot fresh weight in BS recovered to 2.98 kg and rhizome fresh weight to 3.72 kg, representing 73.0% and 41.2% increases over the S treatment. Additionally, the disease index was reduced by 55.26 in BS compared with the control group. Nay more, Bacillus, Chujaibacter, and Rhodanobacter taxa were significantly enriched in BS group. In conclusion, B. subtilis FZ-7 effectively mitigates southern blight in A. carmichaelii by modulating rhizosphere microbial assembly, enriching beneficial taxa, and stabilizing microbial co-occurrence networks, highlighting its potential as a biocontrol agent for sustainable medicinal plant production.