Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 267 This study will integrate the current knowledge of rhizosphere microbiome-assisted breeding, with a focus on the combination of microbial induction and host variety improvement to enhance crop disease resistance. It will review the limitations of traditional crop disease management methods and emphasize the necessity of microbiome-based methods. Clarify the mechanism by which the interaction between rhizosphere microorganisms and plant hosts endows them with disease resistance; Propose a breeding framework that combines microbiome manipulation with host genetic improvement. By bridging plant genetics and microbiome science, this study aims to advance sustainable crop protection strategies and contribute to building resilient agricultural systems. 2 Composition and Functions of Rhizosphere Microbial Communities 2.1 Major microbial groups in the rhizosphere ecosystem The "liveliness" at Genji far exceeded imagination. Here, there are not only bacteria and fungi, but also actinomycetes, archaea, protozoa, and even viruses - although the latter types are often overlooked, they are indeed present. Ultimately, however, the most frequently concerned ones are still bacteria and fungi. Bacteria such as Proteobacteria, actinomycetes and Bacteroides are often detected in the rhizosphere (Ling et al., 2022; Maphosa et al., 2025). Fungi are not simple either. Whether it is mycorrhizal fungi that can help plants absorb phosphorus or saprophytic fungi that live by decomposing organic matter, they are all involved in nutrient cycling and plant interactions (Chauhan et al., 2023). Actinomycetes are also worth mentioning. These microorganisms, which look like "bacterial fungi", can not only produce antibiotics but also improve plant health. Ultimately, whether there are many of these microorganisms and which species prevail largely depends on the plant's own genotype, the composition of root secretions, and the overall condition of the soil and environment (Ren et al., 2025). 2.2 Mutualistic relationships between microbial communities and plant roots Plants themselves also "nurture bacteria". The large amount of substances secreted by the root system - sugars, amino acids, organic acids, secondary metabolites - is like a carefully prepared "menu", attracting various beneficial microorganisms to approach and eventually participating in the construction of the rhitrosphere community. This is not a one-way giving. The microorganisms attracted have shown their respective abilities in helping plants absorb nutrients, stimulating growth and preventing pathogenic bacteria from invading. Probiotic bacteria like PGPR and mycorrhizal fungi, when cooperating with plants, not only have high efficiency but also enhance stress resistance. However, this relationship is not static. Environmental factors, the developmental stage of the plant itself, and even genetic background can all cause fluctuations in this "cooperation". 2.3 Functional roles of beneficial microorganisms in plant disease defense When it comes to disease resistance, plants are not fighting alone. Their "microbial friends" have taken on quite a few tasks in this area - and in many ways. Some directly act, such as some Pseudomonas, Bacillus or actinomycetes, which suppress the growth of pathogenic bacteria by producing antibacterial substances (Lazcano et al., 2021). Some are more like behind-the-scenes commanders, mobilizing the plant's own defense system by inducing systemic resistance (ISR), enabling the plant to respond more quickly when facing different pathogens. Some microorganisms take the lead in occupying resources or space and compete with pathogenic bacteria for territory. Once they win, it becomes very difficult for the pathogenic bacteria to take root. What is more complex is the microbial network in the rhizosphere that checks and balances each other yet collaborates. Its stability and recovery ability themselves can help plants resist diseases. These methods are not mutually exclusive; instead, they often occur simultaneously, forming an "invisible" protective barrier and providing the possibility of reducing reliance on pesticides. 3 Microbe-Induced Systemic Resistance Mechanisms in Plants 3.1 Molecular basis of ISR (induced systemic resistance) and SAR (systemic acquired resistance) Plants do not only become "tough" when they encounter diseases. Sometimes, even when there is no illness or disaster, some "good bacteria" can also activate its immune state in advance. Rhizosphere bacteria like PGPR and certain fungi often play the role of such a "quiet reminder", inducing the ISR response. And immune mechanisms like SAR are usually activated only after pathogen invasion. Ultimately, both can eventually prepare plants in
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