Lai Xianjun, He Zhouhua, Wang Shuyan, Zhang Feng, Wang Haiyan, Wang Xiyao, Liu Shifeng, Yan Lang
Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Liangshan, China.
Potato Research and Development Center, College of Agriculture Science, Sichuan Agricultural University, Chengdu, China.
Front Plant Sci. 2025 May 16;16:1577123. doi: 10.3389/fpls.2025.1577123. eCollection 2025.
Plant root-associated microbiomes play an important role in plant health, yet their responses to bacterial wilt remain unclear poorly understood.
This study investigated spatial variations in microbiome and metabolome composition across three root-associated niches-root-surrounding soil, rhizosphere, and endosphere-of healthy and -infected potato plants. A total of 36 samples were analyzed, with microbial diversity assessed by full-length 16S rRNA and ITS sequencing, and metabolic profiles characterized using LC-QTOF-MS.
Alpha diversity analysis revealed that bacterial diversity in healthy plants was consistently higher than in diseased plants, progressively increasing from the root-surrounding soil to the rhizosphere, and most notably in the endosphere, where the Shannon index declined from 5.3 (healthy) to 1.2 (diseased). In contrast, fungal diversity was lower in diseased plants in the root-surrounding soil and rhizosphere, but significantly elevated in the endosphere, suggesting niche-specific microbial responses to pathogen stress. Beta diversity confirmed significant microbiome restructuring under pathogen stress ( > 0.5, = 0.001). Taxonomic analysis showed over 98% dominance of Proteobacteria in the diseased endosphere, where , , and enriched in healthy plants were significantly reduced. infection promotes the enrichment of species in both the rhizosphere and endosphere. Metabolomic analysis revealed extensive pathogen-induced metabolic reprogramming, with 299 upregulated and 483 downregulated metabolites in the diseased endosphere, including antimicrobial metabolites such as verruculogen and aurachin A. Network analysis identified XTP as a central metabolite regulating microbial interactions, whereas antimicrobial metabolites exhibited targeted pathogen suppression. O2PLS analysis revealed that pathogen-induced antimicrobial metabolites (e.g., Gentamicin X2, Glutathionylspermine) were associated with and in diseased plants, while nucleotide-related compounds (e.g., XTP) correlated with and others, indicating infection-driven microbial adaptation and metabolic restructuring.
These findings provide insights into pathogen-driven disruptions in root microbiomes and suggest potential microbiome engineering strategies for bacterial wilt management.
植物根系相关微生物群在植物健康中发挥着重要作用，但其对青枯病的反应仍不清楚，了解甚少。
本研究调查了健康和感染马铃薯植株的三个根系相关生态位（根际土壤、根际和内生菌）中微生物群和代谢组组成的空间变化。共分析了36个样本，通过全长16S rRNA和ITS测序评估微生物多样性，并使用LC-QTOF-MS对代谢谱进行表征。
α多样性分析表明，健康植株中的细菌多样性始终高于患病植株，从根际土壤到根际逐渐增加，最显著的是在内生菌中，香农指数从5.3（健康）降至1.2（患病）。相比之下，患病植株在根际土壤和根际中的真菌多样性较低，但在内生菌中显著升高，表明微生物对病原体胁迫的生态位特异性反应。β多样性证实了病原体胁迫下微生物群的显著重组（>0.5， = 0.001）。分类学分析表明，患病内生菌中变形菌门的优势度超过98%，健康植株中富集的 、 和 显著减少。 感染促进了根际和内生菌中 物种的富集。代谢组学分析揭示了病原体诱导的广泛代谢重编程，患病内生菌中有299种代谢物上调，483种代谢物下调，包括如疣孢菌素和金耳菌素A等抗菌代谢物。网络分析确定XTP是调节微生物相互作用的核心代谢物，而抗菌代谢物表现出靶向病原体抑制作用。O2PLS分析表明，病原体诱导的抗菌代谢物（如庆大霉素X2、谷胱甘肽精胺）与患病植株中的 和 相关，而核苷酸相关化合物（如XTP）与 和其他物质相关，表明感染驱动的微生物适应和代谢重组。
这些发现为病原体驱动的根系微生物群破坏提供了见解，并提出了潜在的微生物群工程策略用于青枯病管理。
