茅苍术（Atractylodes lancea），菊科苍术属多年生草本植物，药用部位为其干燥的根状茎。因其独特的芳香与化湿功效，在疫病防治中广受欢迎，尤其在《新型冠状病毒肺炎诊疗方案（试行第九版）》推荐的方剂中占据关键位置。与野生品种相比，栽培茅苍术形态与品质显著变化：根状茎由疙瘩结节状转为团块状，须根增多变长，断面“朱砂点”减少且色淡。更重要的是，挥发油在栽培品种中主成分及含量均明显下降，种种表明目前的栽培模式未达到“优质、优形”标准。土壤微生态系统对中药植物形态发育和品质形成影响深远。本研究通过整合同质园跨土壤移植实验，以多组学手段，从生长环境和微生物角度深入探究茅苍术栽培变异成因及调控机制。设置土壤灭菌-回接试验，进一步对微生物功能验证，系统揭示了根际微生物组驱动茅苍术栽培性状变异的分子机制。同时，利用16S rRNA和ITS扩增子技术鉴别不同生境下茅苍术根际核心微生物组，并分析关键土壤环境因子对微生物组结构变异的影响。主要研究结果如下：

不同生境和土壤微生物组对茅苍术的根茎代谢物及转录组产生了显著影响。生境切换（野生→栽培）导致根茎萜类代谢物（Germacrone、Atractylenolide I/II）显著下调，而土壤微生物回接可部分恢复野生型代谢特征。植物激素相关化合物α-亚麻酸（α-Linolenic acid）在栽培生境中普遍上调，与茉莉酸信号通路激活相关。基于转录组-代谢组联合分析发现，土壤微生物跨环境移植显著重塑茅苍术根茎次生代谢网络：野生生境土壤移植（N-C组）诱导萜类标志物（Germacrone等）特异性上调，其合成受MVA途径基因（HMGR1、SQE1）正向调控；而栽培土壤微生物组（C-C组）通过抑制MEP通路基因表达，导致Atractylenolide I等药用成分积累减少。

土壤灭菌-回接试验进一步证实，土壤微生物组的改变对茅苍术的生长、品质及土壤酶活性有着显著影响。野生土壤微生物组通过提高土壤酶活性（如蔗糖酶和酸性磷酸酶）以及植物激素（如IAA和GA3）的含量，促进了光合色素的积累以及挥发油成分（如苍术素和β-桉叶醇）的合成。此外，野生微生物滤液可恢复灭菌土壤中IAA和SA的激素平衡，并通过激活蔗糖酶-叶绿素a协同网络，显著提升苍术酮含量（p < 0.01）。

根际微生物组结构联合土壤环境因子分析表明，野生生境高有机碳（62.08 g/kg）与酸性环境（pH 6.26）维持了Chthoniobacter和Bradyrhizobium等寡营养型酸杆菌的功能优势，其丰度与总碳、铵态氮显著正相关（r=0.82）；而栽培土壤pH升高（7.99）导致Luteitalea等富营养菌群失衡，进而通过负调控萜类合成基因SS3和FTB，降低药材品质。冗余分析表明，TC和pH是驱动微生物群落重构的关键环境因子。

综上所述，本研究首次构建了“土壤因子-核心微生物群-激素信号-代谢通路”四维调控模型，系统阐明了土壤微生物组与生境因子协同调控茅苍术品质形成的机制，为道地药材的微生物定向培育提供理论依据。

Atractylodes lancea, a perennial herbaceous plant in the Atractylodes genus of the Asteraceae family, has its dried rhizome as the medicinal part. Renowned for its unique aroma and dampness-resolving properties, it is widely favored in epidemic prevention and treatment, especially playing a pivotal role in the prescriptions recommended in the “Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (Trial Version 9)”. Compared to wild varieties, cultivated Atractylodes lancea exhibits significant changes in morphology and quality: the rhizome transforms from a knotty and nodular form to a massive one, with increased and elongated fibrous roots, and a reduction in both the number and color intensity of the “cinnabar spots” on the cross-section. More importantly, the main components and content of volatile oils in cultivated varieties have notably decreased, indicating that the current cultivation model does not meet the “high-quality, superior form” standard. The soil microecosystem profoundly influences the morphological development and quality formation of medicinal plants. This study integrates the common garden cross-soil transplantation experiment, employing multi-omics approaches to delve into the causes and regulatory mechanisms of cultivation variations in Atractylodes lancea from the perspectives of growth environment and microorganisms. By setting up soil sterilization-reinoculation tests, it further verifies microbial functions, systematically revealing the molecular mechanisms by which the rhizosphere microbiome drives cultivation trait variations in Atractylodes lancea. Simultaneously, the study utilizes 16S rRNA and ITS amplicon technologies to identify the core rhizosphere microbiome of Atractylodes lancea across different habitats and analyzes the impact of key soil environmental factors on microbiome structural variations. The main research contents are as follows:

Different habitats and soil microbiomes have significantly influenced the rhizome metabolites and transcriptome of Atractylodes lancea. Habitat switching (wild→cultivated) led to a significant downregulation of rhizome terpenoid metabolites (Germacrone, Atractylenolide I/II), while soil microbial reintroduction partially restored the wild-type metabolic characteristics. The plant hormone-related compound α-Linolenic acid was generally upregulated in the cultivated habitat, which is associated with the activation of the jasmonic acid signaling pathway. Transcriptome-metabolome integrated analysis revealed that soil microbial transplantation across environments significantly reshapes the secondary metabolic network in Atractylodes lancea rhizomes: Wild habitat soil transplantation (N-C group) induced specific upregulation of terpenoid markers (e.g., Germacrone), whose synthesis was positively regulated by MVA pathway genes (HMGR1, SQE1); whereas the cultivated soil microbiome (C-C group) led to reduced accumulation of medicinal components such as Atractylenolide I by suppressing MEP pathway gene expression.

The soil sterilization-reinoculation experiment further confirmed that alterations in the soil microbiome significantly impact the growth, quality, and soil enzyme activities of Atractylodes lancea. The wild soil microbiome promoted the accumulation of photosynthetic pigments and the synthesis of volatile oil components, such as atractylodin and β-eudesmol, by enhancing soil enzyme activities (e.g., sucrase and acid phosphatase) and the levels of plant hormones (e.g., IAA and GA3). Additionally, the wild microbial filtrate restored the hormonal balance of IAA and SA in sterilized soil and significantly increased the content of atractylone (p < 0.01) by activating the sucrase-chlorophyll a synergistic network.

The analysis of rhizosphere microbiome structure in conjunction with soil environmental factors revealed that the high organic carbon content (62.08 g/kg) and acidic environment (pH 6.26) in wild habitats maintained the functional dominance of oligotrophic acidobacteria such as Chthoniobacter and Bradyrhizobium, whose abundance was significantly positively correlated with total carbon and ammonium nitrogen (r=0.82). In contrast, the increased pH (7.99) in cultivated soils led to an imbalance of eutrophic bacterial communities such as Luteitalea, which subsequently reduced the quality of medicinal materials by negatively regulating the terpene synthesis genes SS3 and FTB. Redundancy analysis indicated that TC and pH were the key environmental factors driving the reconstruction of microbial communities.

In summary, this study has, for the first time, constructed a four-dimensional regulatory model encompassing “soil factors-core microbiota-hormone signaling-metabolic pathways”. It systematically elucidates the mechanism by which the soil microbiome and habitat factors collaboratively regulate the quality formation of Atractylodes lancea, providing a theoretical basis for the microbial-directed cultivation of authentic medicinal herbs.

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