[1]

Jiang L, Chen Y, Wang X, Guo W, Bi Y, et al. 2022. New insights explain that organic agriculture as sustainable agriculture enhances the sustainable development of medicinal plants. Frontiers in Plant Science 13:959810

doi: 10.3389/fpls.2022.959810
[2]

He L, Zhang S, Yang C, Xu B, Su Z, et al. 2021. 生态扶贫视域下的中药材生态种植论析 [Ecological planting of Chinese medicinal materials from perspective of ecological poverty alleviation view]. 中国现代中药 [Modern Chinese Medicine] 23:417−20 (in Chinese)

doi: 10.13313/j.issn.1673-4890.20201124004
[3]

Wang Y, Zhang Y, Cong H, Li C, Wu J, et al. 2023. Cultivable endophyte resources in medicinal plants and effects on hosts. Life 13:1695

doi: 10.3390/life13081695
[4]

Lv J, Yang S, Zhou W, Liu Z, Tan J, et al. 2024. Microbial regulation of plant secondary metabolites: Impact, mechanisms and prospects. Microbiology Research 283:127688

doi: 10.1016/j.micres.2024.127688
[5]

Zhang WJ, Zhao ZY, Chang LK, Cao Y, Wang S, et al. 2021. Atractylodis Rhizoma: a review of its traditional uses, phytochemistry, pharmacology, toxicology and quality control. Journal of Ethnopharmacology 266:113415

doi: 10.1016/j.jep.2020.113415
[6]

Gu Y, Feng X, Xia B. 2007. Dynamic change of essential oil content and increment in different organs of Atractylodes lancea. Journal of Plant Resources and Environment 16:24−28, 42

doi: 10.3969/j.issn.1674-7895.2007.04.005
[7]

Ouyang L. 2023. Study on the grade standard of Atractylodis Rhizoma. Thesis. Shanghai University of Traditional Chinese Medicine, China. pp. 15-24 doi: 10.27320/d.cnki.gszyu.2020.000736

[8]

Chen LJ, Wu XQ, Xu Y, Wang BL, Liu S, et al. 2021. Microbial diversity and community structure changes in the rhizosphere soils of Atractylodes lancea from different planting years. Plant Signaling & Behavior 16:1854507

doi: 10.1080/15592324.2020.1854507
[9]

Wu H, Lin W. 2020. 药用植物连作障碍研究评述和发展透视 [A commentary and development perspective on the consecutive monoculture problems of medicinal plants]. 中国生态农业学报 [Chinese Journal of Eco-Agriculture] 28:775−93

doi: 10.13930/j.cnki.cjea.190760
[10]

Wang H, Wang Y, Kang C, Wang S, Zhang Y, et al. 2022. Drought stress modifies the community structure of root-associated microbes that improve Atractylodes lancea growth and medicinal compound accumulation. Frontiers in Plant Science 13:1−19

doi: 10.3389/fpls.2022.1032480
[11]

Fang F, Dai C, Zhang B, Liang Q. 2009. 茅苍术悬浮细胞系建立及内生真菌诱导子对其挥发油积累的影响 [Establishment of suspension cell line of At ractylodes lancea and effect of endophytic fungal elicitors on its essential oil accumulation]. 中草药 [Chinese Traditional and Herbal Drugs] 40:452−55

doi: 10.3321/j.issn:0253-2670.2009.03.035
[12]

Yang H. 2022. Study on signal difference of endophytic bacteria promoting volatile oil accumulation in Atractylodes macrocephala and Atractylodes lancea. Thesis. Nanjing Normal University, China. pp. 4−5 doi: 10.27245/d.cnki.gnjsu.2019.002423

[13]

Cao L, Chen F, Dai C. 2022. 茅苍术与内生菌互作信号对其活性成分的影响 [Change of Atractylodes lancea signaling during endogenous microbes colonization effects the genuine active compounds]. 农业环境科学学报 [Journal of Agro-Environment Science] 41:2831−39

doi: 10.11654/jaes.2022-1006
[14]

Fang F, Dai C, Wang Y. 2009. 一氧化氮和过氧化氢在内生真菌小克银汉霉属 AL4 诱导子促进茅苍术细胞挥发油积累中的作用 [Role of nitric oxide and hydrogen peroxide in the essential oil increasing of suspension cells from Atractylodes lancea induced by endophytic fungal Cunninghamella sp. AL4 elicitor]. 生物工程学报 [Chinese Journal of Biotechnology] 25:1490−96

doi: 10.3321/j.issn:1000-3061.2009.10.008
[15]

Wang XM, Yang B, Ren CG, Wang HW, Wang JY, et al. 2015. Involvement of abscisic acid and salicylic acid in signal cascade regulating bacterial endophyte-induced volatile oil biosynthesis in plantlets of Atractylodes lancea. Plant Physiology 153:30−42

doi: 10.1111/ppl.12236
[16]

Bai B, Liu W, Qiu X, Zhang J, Zhang J, et al. 2022. The root microbiome: Community assembly and its contributions to plant fitness. Journal of Integrative Plant Biology 64:230−43

doi: 10.1111/jipb.13226
[17]

Fan X, Ge AH, Qi S, Guan Y, Wang R, et al. 2025. Root exudates and microbial metabolites: signals and nutrients in plant-microbe interactions. Science China Life Sciences 68:2290−302

doi: 10.1007/s11427-024-2876-0
[18]

Srivastava AK, Singh RD, Pandey GK, Mukherjee PK, Foyer CH. 2025. Unravelling the molecular dialogue of beneficial microbe−plant interactions. Plant Cell & Environment 48:2534−48

doi: 10.1111/pce.15245
[19]

Zeng Q, Hu HW, Ge AH, Xiong C, Zhai CC, et al. 2025. Plant−microbiome interactions and their impacts on plant adaptation to climate change. Journal of Integrative Plant Biology 67:826−44

doi: 10.1111/jipb.13863
[20]

Zhang C, Wang S, Sun J, Li X, Wang H, et al. 2024. Genome resequencing reveals the genetic basis of population evolution, local adaptation, and rewiring of the rhizome metabolome in Atractylodes lancea. Horticulture Research 11:uhae167

doi: 10.1093/hr/uhae167
[21]

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550

doi: 10.1186/s13059-014-0550-8
[22]

Wu T, Hu E, Xu S, Chen M, Guo P, et al. 2021. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2:100141

doi: 10.1016/j.xinn.2021.100141
[23]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT Method. Methods 25:402−8

doi: 10.1006/meth.2001.1262
[24]

Chen W, Gao Y, Xie W, Gong L, Lu K, et al. 2014. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics 46:714−21

doi: 10.1038/ng.3007
[25]

Pang Z, Mao X, Zhou S, Yu S, Liu G, et al. 2023. Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage. Microbiome 11:85

doi: 10.1186/s40168-023-01525-x
[26]

Thévenot EA, Roux A, Xu Y, Ezan E, Junot C. 2015. Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. Journal of Proteome Research 14:3322−35

doi: 10.1021/acs.jproteome.5b00354
[27]

Jeon JE, Kim JG, Fischer CR, Mehta N, Dufour-Schroif C, et al. 2020. A pathogen-responsive gene cluster for highly modified fatty acids in tomato. Cell 180:176−187.e19

doi: 10.1016/j.cell.2019.11.037
[28]

Li KP, Yuan M, Wu YL, Pineda M, Zhang CM, et al. 2022. A high-fat high-fructose diet dysregulates the homeostatic crosstalk between gut microbiome, metabolome, and immunity in an experimental model of obesity. Molecular Nutrition & Food Research 66:e2100950

doi: 10.1002/mnfr.202100950
[29]

Yuan J. 2019. The mechanism of endophytic fungus Gilmaniella sp. AL12 promotion of plant growth and sesquiterpenoid accumulation in Atractylodes lancea. Thesis. Nanjing Normal University, China. pp. 4-6 doi: 10.27245/d.cnki.gnjsu.2019.002436

[30]

Sun XL, Xu YF, Ma LY, Zhou H. 2010. 植株叶片的光合色素构成对遮阴的响应 [A review of acclimation of photosynthetic pigment composition in plant leaves to shade environment]. 植物生态学报 [Chinese Journal of Plant Ecology] 34:989−99

doi: 10.3773/j.issn.1005-264x.2010.08.012
[31]

Pandey SS, Singh S, Pandey H, Srivastava M, Ray T, et al. 2018. Endophytes of Withania somnifera modulate in planta content and the site of withanolide biosynthesis. Scientific Reports 8:5450

doi: 10.1038/s41598-018-23716-5
[32]

Hou S, Thiergart T, Vannier N, Mesny F, Ziegler J, et al. 2021. A microbiota-root-shoot circuit favours Arabidopsis growth over defence under suboptimal light. Nature Plants 7:1078−92

doi: 10.1038/s41477-021-00956-4
[33]

Zhou J. 2016. Mechanisms underlying Pseudomonas fluorescens efficiently increasing the sesquiterpenoid content and diversity in Atractylodes lancea. Thesis. Nanjing Normal University, China. pp. 4−7

[34]

Xu S, Dong H, Zeng X, Zhao Z. 2019. 萜类植物源农药的筛选及活性研究进展 [Research progress in screening and bioactivity of terpenoid botanical pesticides]. 林产化学与工业 [Chemistry and Industry of Forest Products] 39:1−12

doi: 10.3969/j.issn.0253-2417.2019.01.001
[35]

Ren CG, Dai CC. 2012. Jasmonic acid is involved in the signaling pathway for fungal endophyte-induced volatile oil accumulation of Atractylodes lancea plantlets. BMC Plant Biology 12:128

doi: 10.1186/1471-2229-12-128
[36]

Ren CG, Dai CC. 2013. Nitric oxide and brassinosteroids mediated fungal endophyte-induced volatile oil production through protein phosphorylation pathways in Atractylodes lancea plantlets. Journal of Integrative Plant Biology 55:1136−46

doi: 10.1111/jipb.12087
[37]

Cui X, Zhao P, Liang W, Cheng Q, Mu B, et al. 2020. A rapeseed WRKY transcription factor phosphorylated by CPK modulates cell death and Leaf senescence by regulating the expression of ROS and SA-synthesis-related genes. The Journal of Agricultural and Food Chemistry 68:7348−59

doi: 10.1021/acs.jafc.0c02500
[38]

Gao X, He P. 2013. Nuclear dynamics of Arabidopsis calcium-dependent protein kinases in effector-triggered immunity. Plant Signaling & Behavior 8:e23868

doi: 10.4161/psb.23868
[39]

Wang D, Wei L, Liu T, Ma J, Huang K, et al. 2023. Suppression of ETI by PTI priming to balance plant growth and defense through an MPK3/MPK6-WRKYs-PP2Cs module. Molecular Plant 16:903−18

doi: 10.1016/j.molp.2023.04.004
[40]

Hao X, Wang S, Fu Y, Liu Y, Shen H, et al. 2024. The WRKY46-MYC2 module plays a critical role in E-2-hexenal-induced anti-herbivore responses by promoting flavonoid accumulation. Plant Communications 5:100734

doi: 10.1016/j.xplc.2023.100734
[41]

Kazan K, Manners JM. 2013. MYC2: the master in action. Molecular Plant 6:686−703

doi: 10.1093/mp/sss128
[42]

Zheng H, Fu X, Shao J, Tang Y, Yu M, et al. 2023. Transcriptional regulatory network of high-value active ingredients in medicinal plants. Trends in Plant Science 28:429−46

doi: 10.1016/j.tplants.2022.12.007
[43]

Wang L, Chen M, Lam PY, Dini-Andreote F, Dai L, et al. 2022. Multifaceted roles of flavonoids mediating plant-microbe interactions. Microbiome 10:233

doi: 10.1186/s40168-022-01420-x
[44]

Hartwig UA, Joseph CM, Phillips DA. 1991. Flavonoids released naturally from alfalfa seeds enhance growth rate of Rhizobium meliloti. Plant Physiology 95:797−803

doi: 10.1104/pp.95.3.797
[45]

Zhang J, Subramanian S, Stacey G, Yu O. 2009. Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti. Plant Journal 57:171−83

doi: 10.1111/j.1365-313X.2008.03676.x
[46]

Begum N, Wang L, Ahmad H, Akhtar K, Roy R, et al. 2022. Co-inoculation of arbuscular mycorrhizal fungi and the plant growth-promoting rhizobacteria improve growth and photosynthesis in tobacco under drought stress by up-regulating antioxidant and mineral nutrition metabolism. Microbial Ecology 83:971−88

doi: 10.1007/s00248-021-01815-7
[47]

Okutani F, Hamamoto S, Aoki Y, Nakayasu M, Nihei N, et al. 2020. Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community. Plant Cell & Environment 43:1036−46

doi: 10.1111/pce.13708
[48]

Schütz V, Frindte K, Cui J, Zhang P, Hacquard S, et al. 2021. Differential impact of plant secondary metabolites on the soil microbiota. Frontiers in Microbiology 12:666010

doi: 10.3389/fmicb.2021.666010
[49]

Yu P, He X, Baer M, Beirinckx S, Tian T, et al. 2021. Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation. Nature Plants 7:481−99

doi: 10.1038/s41477-021-00897-y
[50]

Wang M, Qiu X, Pan X, Li C. 2021. Transcriptional factor-mediated regulation of active component biosynthesis in medicinal plants. Current Pharmaceutical Biotechnology 22:848−66

doi: 10.2174/1389201021666200622121809