Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 266 Case Study Open Access Rhizosphere Microbiome-Assisted Breeding: Integrating Microbial Induction and Host Variety Improvement for Enhanced Disease Resistance Jin Wang 1, Chunyang Zhan 2 1 Tropical Microbial Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Hainan Institute of Biotechnology Haikou, 570206, Hainan, China Corresponding author: chunyang.zhan@hitar.org Molecular Pathogens, 2025, Vol.16, No.6 doi: 10.5376/mp.2025.16.0027 Received: 27 Sep., 2025 Accepted: 11 Nov., 2025 Published: 20 Nov., 2025 Copyright © 2025 Wang and Zhan, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang J., and Zhan C.Y., 2025, Rhizosphere microbiome-assisted breeding: integrating microbial induction and host variety improvement for enhanced disease resistance, Molecular Pathogens, 16(6): 266-275 (doi: 10.5376/mp.2025.16.0027) Abstract The Rhizosphere microbiota plays a core role in plant health, especially in regulating crops' resistance to soil-borne pathogenic substances, which is of great significance. Facing the practical demands of sustainable agricultural development, intermicrobiota assisted breeding, as an emerging strategy, has demonstrated great potential in enhancing the disease resistance of crops by integrating the induction of beneficial microorganisms with the genetic improvement of host varieties. This study systematically reviewed the composition characteristics and ecological functions of the rhizosphere microbial community, expounded the molecular mechanism of induced systemic resistance (ISR), and the influence of plant genetic background on microbial recruitment. It further explored the integrated breeding strategy of "core microorganisms + resistant varieties" And through actual cases such as tomato-Pseudomonas fluorescens and wheat-Bacillus subtilis, the application effect of microbiota intervention in disease-resistant breeding was demonstrated. This research provides a theoretical basis and technical support for the development of a low-dependence pesticide and green, efficient disease-resistant breeding system. Keywords Rhizosphere microbiota; Disease-resistant breeding; Inductive system resistance; Microbiota-plant interaction; Multiomics integration 1 Introduction Plant diseases are not a new problem, but in the current context where global agricultural pressure continues to intensify, the threat they pose to crop yields and food security is particularly intractable. All kinds of prevention and control measures are no longer blank, including chemical pesticides, disease-resistant varieties and crop rotation systems. Almost every one of them has been widely adopted in agricultural practice. But problems arise after long-term use - although pesticides can take effect quickly, they also bring environmental pollution and health risks, and force pathogens to evolve resistance rapidly. As for resistant varieties, they seem safe, but the pathogens develop quickly, and the disease-resistant ones grown often have a short "shelf life". Biological pesticides sound environmentally friendly, but in practical application, they are limited by their stability and range of action. However, nowadays, the focus of research seems to be quietly shifting to the "circle of friends" of plants - rhizosphere microorganisms. The microbial community surrounding the plant root system may seem insignificant, but it plays an increasingly important role in the health and disease resistance of plants. Studies have found that plants do not passively accept these microorganisms but actively "pick people" through root secretions. That is to say, they will attract those microorganisms that can help them resist diseases (Yang et al., 2023). These recruited "Allies" can not only directly suppress pathogens but also enable plants to activate their own defense mechanisms. What's more interesting is that some beneficial bacteria can be passed down from generation to generation, from the mother to the offspring, just like giving plants a natural "disease resistance vaccine" (Araujo et al., 2024). Of course, all of this is not static. The structure of the rhizosphere microbiome constantly changes with the environment and the plant's own conditions. Especially when facing pathogenic bacteria attacks, plants sometimes "reorganize their lineup", allowing more inhibitory bacteria to enter the rhizosphere. This "combat mechanism" of plant-microorganism interaction will ultimately determine whether diseases break out and whether plants can survive (Berendsen et al., 2018).
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