中药鹿茸草是玄参科鹿茸草属沙氏鹿茸草（Monochasma savatieri Franch. ex Maxim.）的干燥地上部分，是中成药“炎宁糖浆”的重要原材料之一，具有良好的清热解毒，消炎止疼的效果。由于沙氏鹿茸草的人工栽培起步较晚，相关栽培管理经验仍不完善，尚无关于其病害及防治措施的系统研究报道。在实际生产过程中，根腐病、灰霉病和叶斑病等病害较为常见，其中以根腐病危害最为严重，对产量和品质造成显著影响。作为典型的土传病害，根腐病在沙氏鹿茸草上的发病机制及综合防控措施研究仍较为薄弱，因此本研究以该病害为主要对象开展系统探讨。为了系统解析根腐病对鹿茸草植株的影响及有效的防治方法，本研究基于高通量测序和非靶向代谢组学技术，并结合病原生物学研究，围绕鹿茸草根腐病病原菌的分离鉴定、植物内生菌群和水提物代谢产物变化分析、防治药剂筛选及抗病性鉴定等方面展开深入研究。主要研究结果如下：

（1）利用高通量测序技术分析了健康与患病鹿茸草植株的内生菌群组成，结果表明，根腐病显著降低了鹿茸草内生真菌群落的多样性、均匀度、系统发育多样性及物种丰富度，并改变了微生物群落结构。UPGMA聚类分析显示，健康植株的菌群组成较为稳定，而患病植株的菌群结构更具异质性，反映了病害对鹿茸草内生菌群生态平衡的破坏。此外，基于非靶向代谢组学技术，系统解析了健康植株与患病植株代谢物的变化，结果发现，氨基酸及其衍生物、黄酮类、有机酸和生物碱在健康植株中显著上调，甾醇类、萜类和脂质代谢物在患病组中上调，KEGG富集分析揭示了关键代谢通路的差异，发现醚类脂质代谢、色氨酸代谢、N-聚糖生物合成、甘油磷脂代谢、亚油酸代谢等通路富集程度较高，提示这些代谢变化可能影响植株的抗病能力和信号调控过程。

（2）从鹿茸草根腐病的组织中分离到了疑似致病菌株，通过活体接种和离体接种确定了致病菌株为GF3-5，提取致病菌的DNA并进行PCR扩增，鉴定鹿茸草根腐病的主要病原菌为Fusarium commune，生物学特性实验结果表明最适培养基为Czapek’s培养基，最适氮源硝酸钠，最适碳源为α-乳糖，最适pH为7，最适培养温度为30℃，最适光照条件为全光照。室内药剂筛选结果表明，恶霉灵、甲霜恶霉灵、戊唑醇和乙蒜素对病原菌Fusarium commune具有显著抑制作用，其中化学杀菌剂中甲霜恶霉灵对致病菌的抑制效果最强，EC₅₀为0.0540 mg·L^-1，生物源杀菌剂中乙蒜素对致病菌的抑制效果最强，EC₅₀为19.081 mg·L^-1。田间防治实验中恶霉灵的田间防治效果最好，病情指数最低，为13.25。此外，从鹿茸草根际土壤中筛选到一株对鹿茸草根腐病致病菌F. commune具有较强拮抗作用的细菌，鉴定为枯草芽孢杆菌(Bacillus subtilis)，其抑菌效果优于市售的生防菌产品。利用GC-MS分析其发酵液粗提物的挥发性成分，鉴定出具有抗菌活性的主要化合物，如十五烷酸（C₁₅H₃₀O₂）、3-甲基氨基-1,2,4-噁唑（C₈H₁₂N₂O₂）和2-乙基-3-甲基-1,4-二氮杂环（C₁₆H₃₀O₂）等，表明该菌株及其代谢产物在生物防治中的应用潜力。

（3）为了筛选抗病种质，本研究建立了科学合理的鹿茸草抗病性鉴定方法，明确了最佳接种方法为灌根法、最佳接种孢子液浓度是10⁶ CFU/mL及最佳的接种材料苗龄为6月龄中苗。使用抗病性鉴定方法对筛选到的四种鹿茸草种质资源进行抗病性鉴定，发现2号种质的抗病表现最佳，接种后病情指数最低，为12.21±1.06，为抗病品种选育提供了参考。

本研究系统解析了鹿茸草根腐病的病原菌生物学特性、植株患病后内生菌群及代谢物变化，并筛选出防效较好的的化学和生物药剂，研究结果为鹿茸草根腐病的精准防控提供了重要理论依据，同时为抗病种质资源的挖掘和育种研究奠定了基础，对鹿茸草产业的可持续发展具有重要意义。

Monochasma savatieri Franch. ex Maxim., a species in the family Scrophulariaceae, is a commonly used traditional Chinese medicine. The dried aerial parts of this plant are an important raw material for the Chinese patent medicine "Yanning Syrup," known for its excellent effects in clearing heat, detoxifying, and relieving inflammation and pain. Due to the relatively recent initiation of artificial cultivation of M. savatieri, cultivation experience remains limited, and there are no reports on the diseases and their control measures for this species. However, in practical cultivation, diseases such as root rot, gray mold, and leaf spot are prevalent, with root rot having the most significant impact on the production of M. savatieri. This study focuses on root rot as the research subject. As a common soil-borne disease, root rot severely affects the yield and quality of M. savatieri. Currently, research on the occurrence mechanisms and integrated control strategies for this disease is limited. To systematically analyze the impact of root rot on M. savatieri plants and effective control methods, this study employed high-throughput sequencing and non-targeted metabolomics techniques, combined with pathogen biology research. The study focuses on pathogen isolation and identification, analysis of changes in plant endophytic microbiota and aqueous extract metabolites, screening of control agents, and evaluation of disease resistance. The main research findings are as follows:

(1) High-throughput sequencing technology was used to analyze the composition of the endophytic fungi in healthy and diseased M. savatieri plants. The results indicated that root rot significantly reduced the diversity, phylogenetic diversity, and species richness of the endophytic fungal community in M. savatieri, while also altering the microbial community structure. UPGMA clustering analysis showed that the microbial community composition in healthy plants was relatively stable, whereas the community structure in diseased plants was more heterogeneous, reflecting the disruption of the ecological balance of the endophytic microbiota by the disease. Additionally, based on non-targeted metabolomics, a systematic analysis of the metabolic changes between healthy and diseased plants was conducted. The results revealed that amino acids and their derivatives, flavonoids, organic acids, and alkaloids were significantly upregulated in healthy plants, while sterols, terpenoids, and lipid metabolites were upregulated in the diseased group. KEGG pathway enrichment analysis identified key metabolic pathways with significant differences, such as ether lipid metabolism, tryptophan metabolism, N-glycan biosynthesis, glycerophospholipid metabolism, and linoleic acid metabolism. These findings suggest that these metabolic changes may affect the plant’s disease resistance and signaling regulation processes.

(2) Suspected pathogenic strains were isolated from the tissue of M. savatieri with root rot. Through in vivo and in vitro inoculations, the pathogenic strain was identified as GF3-5. DNA was extracted from the pathogenic fungus, and PCR amplification confirmed that the main pathogen of M. savatieri root rot was Fusarium commune. Biological characteristic experiments revealed that the optimal culture medium for F. commune was Czapek's medium, with sodium nitrate as the best nitrogen source, α-lactose as the best carbon source, a pH of 7 as the optimal condition, a cultivation temperature of 30°C, and continuous light as the most suitable lighting condition. In indoor pesticide screening experiments, the fungicides metalaxyl-m, dimethomorph, tebuconazole, and ethanethiol showed significant inhibitory effects on Fusarium commune. Among the chemical fungicides, dimethomorph exhibited the strongest inhibitory effect on the pathogen, with an EC₅₀ of 0.0540 mg·L⁻¹. Among the biocontrol agents, ethanethiol demonstrated the strongest inhibitory effect, with an EC₅₀ of 19.081 mg·L⁻¹. In field control experiments, metalaxyl-m had the best field control effect, with the lowest disease index of 13.25. Additionally, a bacterium with strong antagonistic activity against the root rot pathogen F. commune was isolated from the rhizosphere soil of M. savatieri and identified as Bacillus subtilis. This strain exhibited stronger antimicrobial effects than commercial biocontrol products. Using GC-MS analysis of the crude extract from its fermentation broth, major antimicrobial compounds were identified, such as pentadecanoic acid (C₁₅H₃₀O₂), 3-methylamino-1,2,4-oxazole (C₈H₁₂N₂O₂), and 2-ethyl-3-methyl-1,4-diazepane (C₁₆H₃₀O₂). These findings suggest that this bacterium and its metabolites have significant potential for use in biocontrol.

(3) To screen for disease-resistant germplasm, a scientifically sound method for evaluating the disease resistance of M. savatieri was established in this study. The optimal inoculation method was root drenching, with the best spore suspension concentration at 10⁶ CFU/mL and the most suitable seedling age for inoculation being 6-month-old seedlings. Using this disease resistance evaluation method, four selected germplasm resources of M. savatieri were assessed for their disease resistance. It was found that germplasm 2 exhibited the best resistance, with the lowest disease index of 12.21±1.06 after inoculation, this study providing a reference for the breeding of disease-resistant varieties.

This study systematically analyzed the biological characteristics of the pathogen causing root rot in M. savatieri, as well as the changes in the plant's endophytic microbiota and metabolites after infection. Additionally, chemical and biological agents with effective control were screened. The research findings provide an important theoretical basis for the precise prevention and control of root rot in M. savatieri. Moreover, it lays a foundation for the exploration of disease-resistant germplasm resources and breeding studies, which is of significant importance for the sustainable development of the M. savatieri industry.