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.

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.

Background: AS2/LOB transcription factors are central regulators of plant organ development and stress responses, yet their characteristics in the monocot crop Asparagus officinalis remain uncharacterized. Methods: In this study, we leveraged the A. officinalis genome to perform a genome-wide identification and comprehensive characterization of the AS2/LOB family. We identified 20 AoAS genes (AoAS01–AoAS20) and analyzed their physicochemical properties, chromosomal localization, conserved domains and motifs, phylogenetic relationships, gene structures, cis-regulatory elements, duplication history, syntenic relationships, protein–protein interaction networks and expression profiles. Results: Phylogenetic analysis divided the AoAS proteins into two major clades (Class I and Class II), while chromosomal mapping revealed their uneven distribution across eight chromosomes. Analysis of publicly available RNA-seq data showed that 14 AoAS genes exhibit dynamic expression across four developmental stages of the stem (10, 25, 40 and 60 cm), with AoAS11 and AoAS14 consistently displaying high transcript levels. Under drought stress, 12 AoAS genes showed significant transcriptional changes, with AoAS04 and AoAS14 exhibiting the most pronounced expression responses. Conclusions: Together, these results provide a genome-wide portrait of the AS2/LOB family in asparagus, reveal their potential roles in development and drought response, nominate candidate genes for breeding stress-tolerant cultivars, and offer a useful benchmark for molecular breeding in economically important species including peony (Paeonia lactiflora).