Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 270 6 Case Studies: Practical Applications of Microbiome-Assisted Disease-Resistance Breeding 6.1 Tomato–Pseudomonas fluorescens combined strategy for enhancing resistance to bacterial wilt There are many methods to control bacterial wilt in tomatoes, but finding stable and effective means without relying on chemical pesticides has always been a difficult problem. The performance of Pseudomonas fluorescens in this regard is notable, especially when used in combination with other microorganisms, such as T. longibrachiatum. Take the Pf3 strain as an example. After seed treatment, not only can the disease inhibition rate be increased to 62% in greenhouses, but even in the field, a protection effect of 61% can be achieved. Even more surprisingly, the output was still 70% higher than that of the susceptible control group. This indicates that not only has the disease been controlled, but the plant's own state has also been activated - indicators such as the activity of defense enzymes are quite telling (Suresh et al., 2022; Du et al., 2025; Sukmana et al., 2025). Compared with traditional pesticides, this "fungus + fungus" combination is more environmentally friendly and is also suitable for integration into disease-resistant tomato breeding programs. 6.2 Wheat co-cultivation with Bacillus subtilis to improve resistance to root rot Root rot of wheat is hard to prevent, but some soil bacteria, such as Bacillus subtilis, have already shown real potential in prevention and control. Some studies directly treated seeds before sowing, whether using bacteria alone or adding a little salicylic acid, and the results were quite promising - the incidence rate could sometimes be reduced to half or even less of the original, and some experimental groups showed almost no symptoms. Moreover, this treatment method not only controlled the disease but also promoted the growth of the wheat itself. The biomass of both the roots and the above-ground parts was higher, and the plant condition was more stable. Even in the face of drought, it could survive. From a mechanistic perspective, on the one hand, it can inhibit the growth of pathogenic fungi; on the other hand, it may also stimulate the plant's own defense system (Mulk et al., 2022; Xu et al., 2022; Guney et al., 2024; Novikova et al., 2024). This type of bacterial agent may indeed serve as an effective tool for assisting disease-resistant breeding in the future. 6.3 Field analysis of rhizosphere microbial community differences among maize varieties and disease resistance Not all corn varieties have the same "appeal" to the rhizosphere microbiome. Field studies have found that many disease-resistant varieties can form more complex and diverse microbial networks in the rhizosphere region, especially the composition and interaction patterns of bacteria, which are often associated with plants in better health. For instance, some modern corn varieties are clearly better at "attracting" microorganisms that are beneficial for nutrient circulation and pathogen inhibition. This phenomenon is not unique to corn; similar observations have also been made in wheat: the types of rhizosphere bacteria in disease-resistant varieties are more diverse, and the fungal community structure is also different from that of disease-susceptible varieties. These differences do not seem accidental. Instead, they suggest that we can use the rhizosphere microbiome as an indicator to assist in screening crop varieties that are more stable and disease-resistant under natural conditions (Figure 1) (Li et al., 2023; Wen et al., 2025). 7 Technological Platforms and Innovative Breeding Models 7.1 High-throughput omics technologies for rhizosphere microbiome analysis (metagenomics, metabolomics, etc.) In the past, it was difficult to conduct systematic and in-depth research on the rhizosphere microbiome, mainly due to technical limitations. But the situation has changed. With the popularization of high-throughput omics approaches such as metagenomics and metabolomics, researchers can now conduct more detailed disassembly of microbial population structure and metabolic functions. These techniques can not only identify which microorganisms may be beneficial, but also observe the differences in their performance under different plant genotype backgrounds. For example, who is more likely to attract beneficial bacteria and who can maintain microbial activity is no longer a guess (Afridi et al., 2022; Dwivedi et al., 2025). In other words, it is now possible to start from the plant end and select or modify those genotypes that are inherently better at "making friends", which also makes microbiome-assisted breeding truly feasible.
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