Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 272 of optimizing them as a whole (Figure 2) (Xun et al., 2024). However, to be fair, there are still many uncertainties when it comes to promoting it in the fields. Environmental fluctuations and the interaction among the three parties are too complex. It's not the case that just by combining one strain and one variety, it can be applied universally. However, with the improvement of omics methods, the enhancement of phenotypic detection efficiency, and the support of ecological engineering technology, the possibility of this "bidirectional" model becoming feasible in future agriculture is indeed increasing bit by bit. Figure 2 Rhizosphere microbiome-assisted crops integrating the beneficial function of the plant genetic-dominated rhizosphere microbiome. The crop alleles controlling the recruitment of rhizosphere microbes with crop beneficial functions were identified through the large-scale and unbiased methods, such as genome-wide association studies (GWASs); from there, the rhizosphere microbiome-assisted crop varieties will be bred (Adopted from Xun et al., 2024) 8 Conclusion and Future Perspectives In the past, the issue of plant disease resistance mainly relied on traditional breeding or genetic modification. However, in recent years, the significance of the plant microbiome has been increasingly recognized - it is not merely a supplementary means; in some scenarios, it is even more crucial. Beneficial microorganisms can compete for nutrients, suppress pathogens, and mobilize the plant's own immune system. These characteristics make them highly promising in sustainable agriculture. Especially with the development of high-throughput sequencing and synthetic biology, scientists have begun to attempt to "customize" microbial communities, and the breeding concept has also quietly changed: no longer focusing only on the plants themselves, but viewing the entire "plant + microorganism" as a consortium (or whole-genome unit) to select resistance resources. However, to be fair, it's not easy to actually apply these "good ideas" from the laboratories to the fields. Microbial communities are alive. When the environment changes, their structure and function may also change accordingly, and their stability is not easy to control. Given that factors such as soil, climate and crop varieties are already complex, the difficulty of predicting the performance of the microbiome in the field can be imagined. At present, many studies are still confined to greenhouses or controlled conditions and are still a bit far from being truly "implemented". To solve these problems, merely discovering beneficial bacteria is not enough. It is also necessary to understand exactly how they interact with plants and design microbial management methods that can operate stably in real agricultural scenarios. Looking ahead, precision agriculture might be one of the breakthroughs. The combination of omics, AI and ecological engineering technologies may find smarter ways to regulate the matching relationship between plants and microorganisms, thereby more efficiently improving crop health. In this process, it is impossible to handle it
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