Metagenomic studies: the physiological perspectives in medicinal and aromatic plants

*Article not assigned to an issue yet

, ,


Review Articles | Published:

E-ISSN: 2229-4473.
Website: www.vegetosindia.org
Pub Email: contact@vegetosindia.org
DOI: 10.1007/s42535-025-01585-4
First Page: 0
Last Page: 0
Views: 1

Keywords: Metagenomics, Medicinal and aromatic plants, Plant secondary metabolism, Secondary metabolites, Phytomicrobiome, Omics, Physiological activities


Abstract


The medicinal and aromatic plants (MAPs) offer a wide range of remedies for various health conditions, owing to the presence of distinctive secondary metabolites, such as phenolics, alkaloids, saponins, terpenes, flavonoids, glycosides, and essential oils. Diverse microbial communities associated with MAPs, whether mutualistic, symbiotic, or neutral, substantially influence plant growth and development, thereby determining the quality and quantity of secondary metabolite production.The advent of metagenomics and other omics-based approaches has greatly advanced our understanding of the intricate interactions between medicinal and aromatic plants and their associated microbiomes. As a result, these approaches enable the characterization of microbial diversity, community composition, metabolic functions, and the discovery of novel taxa, along with insights into their physiological and biochemical attributes. Although numerous comprehensive reviews have addressed the applications of metagenomics in food crops, similar studies focusing on MAPs remain limited. This narrative review aims to examine the beneficial effects of plant–microbe associations in MAPs, with particular emphasis on their physiological impacts, including secondary metabolite production, induction of resistance, environmental adaptation, nutrient uptake, and phytohormone regulation. Such interactions hold considerable potential for enhancing key physiological traits, including biomass accumulation, essential oil yield, secondary metabolite production, and stress tolerance in economically important crops. Beyond advancing sustainable and eco-friendly agricultural practices, these approaches also hold significant potential for applications in medicine and biotechnology.

Metagenomics, Medicinal and aromatic plants, Plant secondary metabolism, Secondary metabolites, Phytomicrobiome, Omics, Physiological activities


References


Abdelfattah A, Wisniewski M, Schena L, Tack AJM (2021) Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root. Environ Microbiol 23(4):2199–2214. https://doi.org/10.1111/1462-2920.15392


Abram F (2015) Systems-based approaches to unravel multi-species microbial community functioning. Comput Struct Biotechnol J. https://doi.org/10.1016/j.csbj.2014.11.009


Acharya-Patel N, Allison MJ, Helbing CC (2022) Environmental DNA: revolutionizing ecological assessments with genomics. In: Genomics and the global bioeconomy. https://doi.org/10.1016/B978-0-323-91601-1.00004-3


Adeleke BS, Muller D, Babalola OO (2023) A metagenomic lens into endosphere microbial communities, promises, and discoveries. Lett Appl Microbiol 76(2):ovac030. https://doi.org/10.1093/lambio/ovac030


Akinsanya MA, Goh JK, Lim SP, Ting ASY (2015) Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genom Data 6:159. https://doi.org/10.1016/j.gdata.2015.09.004


Alahmad A, Harir M, Fochesato S, Tulumello J, Walker A, Barakat M, Ndour PMS, Schmitt-Kopplin P, Cournac L, Laplaze L, Heulin T, Achouak W (2024) Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet. Microbiome 12:1. https://doi.org/10.1186/s40168-023-01727-3


Alreedy RM (2022) Influence of irrigation water on the diversity and distribution of the endophytic bacterial microbiome associated with Mentha longifolia; metagenomics profiling. Egypt J Bot. https://doi.org/10.21608/ejbo.2022.102867.1821


Alsaedi ZS, Ashy RA, Shami AY, Majeed MA, Alswat AM, Baz L, Baeshen MN, Jalal RS (2022) Metagenomic study of the communities of bacterial endophytes in the desert plant Senna italica and their role in abiotic stress resistance in the plant. Braz J Biol 82:e267584. https://doi.org/10.1590/1519-6984.267584


Alswat AM, Jalal RS, Shami AY, Majeed MA, Alsaedi ZS, Baz L, Refai MY, Baeshen MN, Bataweel NM, Al-Hejin A, Ashy RA (2023) Investigating the metagenomics of the bacterial communities in the rhizosphere of the desert plant Senna italica and their role as plant growth promoting factors. Not Bot Horti Agrobot Cluj-Napoca. https://doi.org/10.15835/nbha51113053


Ambardar S, Singh HR, Gowda M, Vakhlu J (2016) Comparative metagenomics reveal phylum level temporal and spatial changes in mycobiome of belowground parts of Crocus sativus. PLoS ONE 11:e0163300. https://doi.org/10.1371/journal.pone.0163300


Ansary WR, Prince FRK, Haque E, Sultana F, West HM, Rahman M, Mondol AM, Akanda AM, Rahman M, Clarke ML, Islam T (2018) Endophytic Bacillus spp. from medicinal plants inhibit mycelial growth of Sclerotinia sclerotiorum and promote plant growth. Z Naturforschung C. https://doi.org/10.1515/znc-2018-0002


Aroca R, Ruiz-Lozano JM (2009) Induction of plant tolerance to semi-arid environments by beneficial soil microorganisms—a review. In: Climate change, intercropping, pest control and beneficial microorganisms. https://doi.org/10.1007/978-90-481-2716-0_7


Bakshi A, Moin M, Madhav MS (2020) Metagenomics in agriculture: state-of-the-art. In: Metagenomics: techniques, applications, challenges and opportunities. https://doi.org/10.1007/978-981-15-6529-8_11


Bashir Y, Pradeep Singh S, Kumar Konwar B (2014) Metagenomics: an application based perspective. Chin J Biol 2014:146030. https://doi.org/10.1155/2014/146030


Bharti N, Yadav D, Barnawal D, Maji D, Kalra A (2013) Exiguobacterium oxidotolerans, a halotolerant plant growth promoting rhizobacteria, improves yield and content of secondary metabolites in Bacopa monnieri (L.) Pennell under primary and secondary salt stress. World J Microbiol Biotechnol. https://doi.org/10.1007/s11274-012-1192-1


Bilal T, Malik B, Hakeem KR (2018) Metagenomic analysis of uncultured microorganisms and their enzymatic attributes. J Microbiol Methods. https://doi.org/10.1016/j.mimet.2018.11.014


Brader G, Compant S, Vescio K, Mitter B, Trognitz F, Ma LJ, Sessitsch A (2017) Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes. Annu Rev Phytopathol. https://doi.org/10.1146/annurev-phyto-080516-035641


Busby PE, Ridout M, Newcombe G (2016) Fungal endophytes: modifiers of plant disease. Plant Mol Biol 90:645. https://doi.org/10.1007/s11103-015-0412-0


Çakmakçı R, Mosber G, Milton AH, Alatürk F, Ali B (2020) The effect of auxin and auxin-producing bacteria on the growth, essential oil yield, and composition in medicinal and aromatic plants. Curr Microbiol 77(4):564–577. https://doi.org/10.1007/s00284-020-01917-4


Ceccarelli N, Curadi M, Martelloni L, Sbrana C, Picciarelli P, Giovannetti M (2010) Mycorrhizal colonization impacts on phenolic content and antioxidant properties of artichoke leaves and flower heads two years after field transplant. Plant Soil 335:311. https://doi.org/10.1007/s11104-010-0417-z


Chakravorty S, Helb D, Burday M, Connell N, Alland D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69:330. https://doi.org/10.1016/j.mimet.2007.02.005


Chen H, Wu H, Yan B, Zhao H, Liu F, Zhang H, Sheng Q, Miao F, Liang Z (2018) Core microbiome of medicinal plant Salvia miltiorrhiza seed: a rich reservoir of beneficial microbes for secondary metabolism. Int J Mol Sci 19(3):672. https://doi.org/10.3390/ijms19030672


Clark DP, Pazdernik NJ, McGehee MR (2019) Genomics and systems biology. In: Molecular biology. https://doi.org/10.1016/b978-0-12-813288-3.00009-4


Cloete KJ, Valentine AJ, Stander MA, Blomerus LM, Botha A (2009) Evidence of symbiosis between the soil yeast Cryptococcus laurentii and a sclerophyllous medicinal shrub, Agathosma betulina (berg.) pillans. Microb Ecol. https://doi.org/10.1007/s00248-008-9457-9


Compant S, Cambon MC, Vacher C, Mitter B, Samad A, Sessitsch A (2021) The plant endosphere world—bacterial life within plants. Environ Microbiol 23(4):1812–1829. https://doi.org/10.1111/1462-2920.15240


Dang H, Zhang T, Li G, Mu Y, Lv X, Wang Z, Zhuang L (2020) Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year. BMC Microbiol 20:291. https://doi.org/10.1186/s12866-020-01977-3


Dastogeer KMG, Tumpa FH, Sultana A, Akter MA, Chakraborty A (2020) Plant microbiome—an account of the factors that shape community composition and diversity. Curr Plant Biol. https://doi.org/10.1016/j.cpb.2020.100161


Dastogeer KMG, Li H, Sivasithamparam K, Jones MGK, Wylie SJ (2018) Fungal endophytes and a virus confer drought tolerance to Nicotiana benthamiana plants through modulating osmolytes, antioxidant enzymes and expression of host drought responsive genes. Environ Exp Bot 149:95. https://doi.org/10.1016/j.envexpbot.2018.02.009


Dharni S, Srivastava AK, Samad A, Patra DD (2014) Impact of plant growth promoting Pseudomonas monteilii PsF84 and Pseudomonas plecoglossicida PsF610 on metal uptake and production of secondary metabolite (monoterpenes) by rose-scented geranium (Pelargonium graveolenscv. bourbon) grown on tannery sludge amended soil. Chemosphere. https://doi.org/10.1016/j.chemosphere.2014.08.001


Dong L, Xu J, Li Y, Fang H, Niu W, Li X, Zhang Y, Ding W, Chen S (2018) Manipulation of microbial community in the rhizosphere alleviates the replanting issues in Panax ginseng. Soil Biol Biochem 125:64. https://doi.org/10.1016/j.soilbio.2018.06.028


Du J, Li Y, Yin Z, Wang H, Zhang X, Ding X (2020) High-throughput customization of plant microbiomes for sustainable agriculture. Front Plant Sci. https://doi.org/10.3389/fpls.2020.569742


Ekor M (2014) The growing use of herbal medicines: issues relating to adverse reactions and challenges in monitoring safety. Front Neurol. https://doi.org/10.3389/fphar.2013.00177


Eljounaidi K, Lee SK, Bae H (2016) Bacterial endophytes as potential biocontrol agents of vascular wilt diseases—review and future prospects. Biol Control. https://doi.org/10.1016/j.biocontrol.2016.07.013


Fadiji AE, Babalola OO (2020) Metagenomics methods for the study of plant-associated microbial communities: a review. J Microbiol Methods 170:105860. https://doi.org/10.1016/j.mimet.2020.105860


Fouda AH, Hassan SED, Eid AM, Ewais EED (2015) Biotechnological applications of fungal endophytes associated with medicinal plant Asclepias sinaica (Bioss.). Ann Agric Sci. https://doi.org/10.1016/j.aoas.2015.04.001


Frank AC, Guzmán JPS, Shay JE (2017) Transmission of bacterial endophytes. Microorganisms. https://doi.org/10.3390/microorganisms5040070


Friesen ML, Porter SS, Stark SC, Von Wettberg EJ, Sachs JL, Martinez-Romero E (2011) Microbially mediated plant functional traits. Annu Rev Ecol Evol Syst 42(1):23–46. https://doi.org/10.1146/annurev-ecolsys-102710-145039


Geneva MP, Stancheva IV, Boychinova MM, Mincheva NH, Yonova PA (2010) Effects of foliar fertilization and arbuscular mycorrhizal colonization on Salvia officinalis L. growth, antioxidant capacity, and essential oil composition. J Sci Food Agric. https://doi.org/10.1002/jsfa.3871


Ghorbanpour M, Hatami M, Khavazi K (2013) Role of plant growth promoting rhizobacteria on antioxidant enzyme activities and tropane alkaloid production of Hyoscyamus niger under water deficit stress. Turkish J Biol 37:350. https://doi.org/10.3906/biy-1209-12


Giri B, Kapoor R, Mukerji KG (2003) Influence of arbuscular mycorrhizal fungi and salinity on growth, biomass, and mineral nutrition of Acacia auriculiformis. Biol Fertil Soils 38:170. https://doi.org/10.1007/s00374-003-0636-z


Gouda S, Das G, Sen SK, Shin HS, Patra JK (2016) Endophytes: a treasure house of bioactive compounds of medicinal importance. Front Microbiol. https://doi.org/10.3389/fmicb.2016.01538


Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245. https://doi.org/10.1016/S1074-5521(98)90108-9


Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669. https://doi.org/10.1128/mmbr.68.4.669-685.2004


Heidari M, Mousavinik SM, Golpayegani A (2011) Plant growth promoting rhizobacteria (PGPR) effect on physiological parameters and mineral uptake in basil (Ociumum basilicm L.) under water stress. J Agric Biol Sci 6


Hemashenpagam N, Selvaraj T (2011) Effect of arbuscular mycorrhizal (AM) fungus and plant growth promoting rhizomicroorganisms (PGPR’s) on medicinal plant Solanum viarum seedlings. J Environ Biol 32:579


Hong CE, Kim JU, Lee JW, Bang KH, Jo IH (2019) Metagenomic analysis of bacterial endophyte community structure and functions in Panax ginseng at different ages. 3 Biotech. https://doi.org/10.1007/s13205-019-1838-x


Hussein RA, El-Anssary AA (2019) Plants secondary metabolites: the key drivers of the pharmacological actions of medicinal plants. Herb Med 1(3):11–30. https://doi.org/10.5772/intechopen.76139


Inbaraj MP (2021) Plant-microbe interactions in alleviating abiotic stress—a mini review. Front Agron 3:667903. https://doi.org/10.3389/fagro.2021.667903


Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D (2022) Potential use of microbial community genomes in various dimensions of agriculture productivity and its management: a review. Front Microbiol 13:708335. https://doi.org/10.3389/fmicb.2022.708335


Jacoby RP, Koprivova A, Kopriva S (2021) Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. J Exp Bot 72(1):57–69. https://doi.org/10.1093/jxb/eraa424


Jaleel CA, Manivannan P, Sankar B, Kishorekumar A, Gopi R, Somasundaram R, Panneerselvam R (2007) Pseudomonas fluorescens enhances biomass yield and ajmalicine production in Catharanthus roseus under water deficit stress. Colloids Surf B Biointerfaces 60(1):7–11. https://doi.org/10.1016/j.colsurfb.2007.05.012


Jamshidi-Kia F, Lorigooini Z, Amini-Khoei H (2018) Medicinal plants: past history and future perspective. J HerbMed Pharmacol. https://doi.org/10.15171/jhp.2018.01


Jan R, Asaf S, Numan M, Lubna Kim KM (2021) Plant secondary metabolite biosynthesis and transcriptional regulation in response to biotic and abiotic stress conditions. Agronomy. https://doi.org/10.3390/agronomy11050968


Khan AL, Al-Harrasi A, Al-Rawahi A, Al-Farsi Z, Al-Mamari A, Waqas M, Asaf S, Elyassi A, Mabood F, Shin JH, Lee IJ (2016) Endophytic fungi from frankincense tree improves host growth and produces extracellular enzymes and indole acetic acid. PLoS ONE 11(6):e0158207. https://doi.org/10.1371/journal.pone.0158207


Khan AL, Gilani SA, Waqas M, Al-Hosni K, Al-Khiziri S, Kim YH, Ali L, Kang SM, Asaf S, Shahzad R, Hussain J, Lee IJ, Al-Harrasi A (2017) Endophytes from medicinal plants and their potential for producing indole acetic acid, improving seed germination and mitigating oxidative stress. J Zhejiang Univ Sci B 18(2):125–137. https://doi.org/10.1631/jzus.B1500271


Khan AL, Asaf S, Abed RMM, Chai YN, Al-Rawahi AN, Mohanta TK, Al-Rawahi A, Schachtman DP, Al-Harrasi A (2020) Rhizosphere microbiome of arid land medicinal plants and extra cellular enzymes contribute to their abundance. Microorganisms 8(2):213. https://doi.org/10.3390/microorganisms8020213


Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA (2020) Emerging priorities for microbial metagenome research. Bioresour Technol Rep 11:100485. https://doi.org/10.1016/j.biteb.2020.100485


Köberl M, Schmidt R, Ramadan EM, Bauer R, Berg G (2013) The microbiome of medicinal plants: diversity and importance for plant growth, quality, and health. Front Microbiol. https://doi.org/10.3389/fmicb.2013.00400


Kumar GC, Chaudhary J, Meena LK, Meena AL, Kumar A (2021) Function-driven microbial genomics for ecofriendly agriculture. In: Microbes in land use change management. https://doi.org/10.1016/B978-0-12-824448-7.00021-8


Kumar GR, Shiwangi S, Chanotiya CS, Kapil D, Kumar TP, Akanksha S (2024) Diversity and functional characterization of endophytes in two contrasting cultivars of Ocimum sanctum: Insights from culture based and metagenomic approaches. J Plant Growth Regul


Liben W (2023) An overview of host microbes interaction. Int Res J Microbiol 12:1–3


Liu C, Yu J, Ying J, Zhang K, Hu Z, Liu Z, Chen S (2023) Integrated metagenomics and metabolomics analysis reveals changes in the microbiome and metabolites in the rhizosphere soil of Fritillaria unibracteata. Front Plant Sci 14:1223720. https://doi.org/10.3389/fpls.2023.1223720


Lu Y, Zhang E, Hong M, Yin X, Cai H, Yuan L, Yuan F, Li L, Zhao K, Lan X (2020) Analysis of endophytic and rhizosphere bacterial diversity and function in the endangered plant Paeonia ludlowii. Arch Microbiol 202:1717. https://doi.org/10.1007/s00203-020-01882-3


Lugtenberg B, Rozen DE, Kamilova F (2017) Wars between microbes on roots and fruits. F1000Res. https://doi.org/10.12688/f1000research.10696.1


Maggini V, De Leo M, Mengoni A, Gallo ER, Miceli E, Reidel RVB, Biffi S, Pistelli L, Fani R, Firenzuoli F, Bogani P (2017) Plant-endophytes interaction influences the secondary metabolism in Echinacea purpurea (L.) Moench: an in vitro model. Sci Rep. https://doi.org/10.1038/s41598-017-17110-w


Mandal S, Evelin H, Giri B, Singh VP, Kapoor R (2013) Arbuscular mycorrhiza enhances the production of stevioside and rebaudioside-A in Stevia rebaudiana via nutritional and non-nutritional mechanisms. Appl Soil Ecol 72:187. https://doi.org/10.1016/j.apsoil.2013.07.003


Marin M, Ybarra M, Fé A, García-Férriz L (2002) Effect of arbuscular mycorrhizal fungi and pesticides on Cynara cardunculus growth. Agric Food Sci Finland 11. https://doi.org/10.23986/afsci.5728


Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33:1437. https://doi.org/10.1016/S0038-0717(01)00052-9


Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, Elbourne LDH, LeTourneau MK, Gang DR, Paulsen IT, Weller DM, Thomashow LS, Flynt AS, Mavrodi DV (2021) Root exudates alter the expression of diverse metabolic, transport, regulatory, and stress response genes in rhizosphere Pseudomonas. Front Microbiol 12:651282. https://doi.org/10.3389/fmicb.2021.651282


Mehabo PM (2012) Culture-independent characterization of endophytic bacterial communities associated with a South African medicinal plant. University of Johannesburg, Dicoma anomala


Mengoni A, Maida I, Chiellini C, Emiliani G, Mocali S, Fabiani A, Fondi M, Firenzuoli F, Fani R (2014) Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs. Res Microbiol 165:686. https://doi.org/10.1016/j.resmic.2014.09.008


Wani AK, Rahayu F, Alkahtani AM, Alreshidi MA, Yadav KK, Fauziah L, Murianingrum M, Akhtar N, Mufidah E, Rahayu DM, Singh R (2024) Metagenomic profiling of rhizosphere microbiota: unraveling the plant-soil dynamics. Physiol Molecular Plant Pathol 1(133):102381


Moënne-Loccoz Y, Mavingui P, Combes C, Normand P, Steinberg C (2015) Microorganisms and biotic interactions. In: Environmental microbiology: fundamentals and applications. https://doi.org/10.1007/978-94-017-9118-2_11


Nishad R, Ahmed T, Rahman VJ, Kareem A (2020) Modulation of plant defense system in response to microbial interactions. Front Microbiol. https://doi.org/10.3389/fmicb.2020.01298


Nwachukwu BC, Babalola OO (2021) Perspectives for sustainable agriculture from the microbiome in plant rhizosphere. Plant Biotechnol Rep. https://doi.org/10.1007/s11816-021-00676-3


Nwachukwu BC, Babalola OO (2022) Metagenomics: a tool for exploring key microbiome with the potentials for improving sustainable agriculture. Front Sustain Food Syst. https://doi.org/10.3389/fsufs.2022.886987


Oberhofer M, Hess J, Leutgeb M, Gössnitzer F, Rattei T, Wawrosch C, Zotchev SB (2019) Exploring actinobacteria associated with rhizosphere and endosphere of the native alpine medicinal plant Leontopodium nivale subspecies alpinum. Front Microbiol 10:2531. https://doi.org/10.3389/fmicb.2019.02531


Ortíz-Castro R, Contreras-Cornejo HA, Macías-Rodríguez L, López-Bucio J (2009) The role of microbial signals in plant growth and development. Plant Signal Behav 4(8):701–712. https://doi.org/10.4161/psb.4.8.9047


Pérez-Cobas AE, Gomez-Valero L, Buchrieser C (2020) Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 6:e000409. https://doi.org/10.1099/mgen.0.000409


Piombo E, Abdelfattah A, Droby S, Wisniewski M, Spadaro D, Schena L (2021) Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms 9:188. https://doi.org/10.3390/microorganisms9010188


Prasad R, Kamal S, Sharma PK, Oelmüller R, Varma A (2013) Root endophyte Piriformospora indica DSM 11827 alters plant morphology, enhances biomass and antioxidant activity of medicinal plant Bacopa monniera. J Basic Microbiol 53:1016. https://doi.org/10.1002/jobm.201200367


Qi X, Wang E, Xing M, Zhao W, Chen X (2012) Rhizosphere and non-rhizosphere bacterial community composition of the wild medicinal plant Rumex patientia. World J Microbiol Biotechnol 28:2257. https://doi.org/10.1007/s11274-012-1033-2


Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. https://doi.org/10.1038/nbt.3935


Ramadan AM, Nazar MAH, Gadallah NO (2021) Metagenomic analysis of rhizosphere bacteria in desert plant Calotropis procera. Geomicrobiol J 38:375. https://doi.org/10.1080/01490451.2020.1860166


Ramlal A, Rani A, Nautiyal A, Kalra C, Kumari R, Kumar J, Veeranna S, Mishra V (2023) Importance of omics approaches in plant-microbe interaction for plant disease control. Physiol Mol Plant Pathol. https://doi.org/10.1016/j.pmpp.2023.102153


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 Biol 12:128. https://doi.org/10.1186/1471-2229-12-128


Rho H, Kim SH (2017) Endophyte effects on photosynthesis and water use of plant hosts: a meta-analysis. In: Functional Importance of the plant microbiome: implications for agriculture, forestry and bioenergy. https://doi.org/10.1007/978-3-319-65897-1_4


Rodriguez RJ, Henson J, Van Volkenburgh E, Hoy M, Wright L, Beckwith F, Kim YO, Redman RS (2008) Stress tolerance in plants via habitat-adapted symbiosis. ISME J 2(4):404–416. https://doi.org/10.1038/ismej.2007.106


Saha L, Tiwari J, Bauddh K, Ma Y (2021) Recent developments in microbe–plant-based bioremediation for tackling heavy metal-polluted soils. Front Microbiol. https://doi.org/10.3389/fmicb.2021.731723


Santoro MV, Cappellari LR, Giordano W, Banchio E (2015) Plant growth-promoting effects of native Pseudomonas strains on Mentha piperita (peppermint): an in vitro study. Plant Biol 17(6):1218–1226. https://doi.org/10.1111/plb.12351


Sauer S, Dlugosch L, Kammerer DR, Stintzing FC, Simon M (2021) The microbiome of the medicinal plants Achillea millefolium L. and Hamamelis virginiana L. Front Microbiol. https://doi.org/10.3389/fmicb.2021.696398


Senn S, Pangell K, Bowerman AL (2022) Metagenomic insights into the composition and function of microbes associated with the rootzone of Datura inoxia. Biotech 11:1. https://doi.org/10.3390/BIOTECH11010001


Sharma M, Sudheer S, Usmani Z, Rani R, Gupta P (2020) Deciphering the omics of plant-microbe interaction: perspectives and new insights. Curr Genom 21:343. https://doi.org/10.2174/1389202921999200515140420


Shi JY, Yuan XF, Lin HR, Yang YQ, Li ZY (2011) Differences in soil properties and bacterial communities between the rhizosphere and bulk soil and among different production areas of the medicinal plant Fritillaria thunbergii. Int J Mol Sci 12(6):3770–3785. https://doi.org/10.3390/ijms12063770


Shi X, Zhao Y, Xu M, Ma L, Adams JM, Shi Y (2024) Insights into plant–microbe interactions in the rhizosphere to promote sustainable agriculture in the new crops era. New Crops 1:100004. https://doi.org/10.1016/j.ncrops.2023.11.002


Sofowora A, Ogunbodede E, Onayade A (2013) The role and place of medicinal plants in the strategies for disease prevention. Afr J Tradit Complement Altern Med 10:210. https://doi.org/10.4314/ajtcam.v10i5.2


Stelmasiewicz M, Świątek Ł, Gibbons S, Ludwiczuk A (2023) Bioactive compounds produced by endophytic microorganisms associated with bryophytes—the “Bryendophytes.” Molecules 28(7):3246. https://doi.org/10.3390/molecules28073246


Sun RT, Feng XC, Zhang ZZ, Zhou N, Feng HD, Liu YM, Hashem A, Al-Arjani ABF, Abd-Allah EF, Wu QS (2022) Root endophytic fungi regulate changes in sugar and medicinal compositions of Polygonum cuspidatum. Front Plant Sci. https://doi.org/10.3389/fpls.2022.818909


Tamang A, Swarnkar M, Kumar P, Kumar D, Pandey SS, Hallan V (2023) Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb. Microbiol Spectr 11:e02279. https://doi.org/10.1128/spectrum.02279-23


Meng LL, Liu RC, Yang L, Zou YN, Srivastava AK, Kuča K, Hashem A, Abd-Allah EF, Giri B, Wu QS (2021) The change in fatty acids and sugars reveals the association between trifoliate orange and endophytic fungi. J Fungi 7:716


Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis. Microb Inform Exp 2(1):3. https://doi.org/10.1186/2042-5783-2-3


Tiwari S, Lata C (2018) Heavy metal stress, signaling, and tolerance due to plant-associated microbes: an overview. Front Plant Sci. https://doi.org/10.3389/fpls.2018.00452


Tkalec V, Mahnic A, Gselman P, Rupnik M (2022) Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approaches. Folia Microbiol (Praha). https://doi.org/10.1007/s12223-022-00958-5


Tshikhudo PP, Ntushelo K, Mudau FN (2023) Sustainable applications of endophytic bacteria and their physiological/biochemical roles on medicinal and herbal plants: review. Microorganisms 11(2):453. https://doi.org/10.3390/microorganisms11020453


Urumbil SK, Anilkumar M (2021) Metagenomic insights into plant growth promoting genes inherent in bacterial endophytes of Emilia sonchifolia (Linn.) DC. Plant Sci Today. https://doi.org/10.14719/pst.1357


Villalobos-Flores LE, Espinosa-Torres SD, Hernández-Quiroz F, Piña-Escobedo A, Cruz-Narváez Y, Velázquez-Escobar F, Süssmuth R, García-Mena J (2022) The bacterial and fungal microbiota of the mexican rubiaceae family medicinal plant Bouvardia ternifolia. Microb Ecol 84(2):510–526. https://doi.org/10.1007/s00248-021-01871-z


Wagner MR, Lundberg DS, Del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun 7(1):12151. https://doi.org/10.1038/ncomms12151


Wang XM, Yang B, Ren CG, Wang HW, Wang JY, Dai CC (2015) Involvement of abscisic acid and salicylic acid in signal cascade regulating bacterial endophyte-induced volatile oil biosynthesis in plantlets of Atractylodes lancea. Physiol Plant 153(1):30–42. https://doi.org/10.1111/ppl.12236


Wani AK, Qadir F, Elboughdiri N, Rahayu F, Pranowo D, Martasari C, Kosmiatin M, Suhara C, Sudaryono T, Prayogo Y, Yadav KK (2025) Metagenomics and plant-microbe symbioses: microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health. Biotechnol Adv 15:108580


White JF, Kingsley KL, Zhang Q, Verma R, Obi N, Dvinskikh S, Elmore MT, Verma SK, Gond SK, Kowalski KP (2019) Review: endophytic microbes and their potential applications in crop management. Pest Manag Sci. https://doi.org/10.1002/ps.5527


Wu X, Yang Y, Zhang H (2023) Microbial fortification of pharmacological metabolites in medicinal plants. Comput Struct Biotechnol J. https://doi.org/10.1016/j.csbj.2023.10.024


Wu L, Chen J, Wu H, Wang J, Wu Y, Lin S, Khan MU, Zhang Z, Lin W (2016) Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing. Sci Rep 6:26601. https://doi.org/10.1038/srep26601


Wu L, Wang J, Wu H, Chen J, Xiao Z, Qin X, Zhang Z, Lin W (2018) Comparative metagenomic analysis of rhizosphere microbial community composition and functional potentials under Rehmannia glutinosa consecutive monoculture. Int J Mol Sci 19:2394. https://doi.org/10.3390/ijms19082394


Xiao J et al (2025) Mechanistic insights from metagenomics into the early-stage quality improvement of licorice under partial replacement of chemical by organic fertilizers. Front Plant Sci. https://doi.org/10.3389/fpls.2025.1613771


Xiong W, Li Z, Liu H, Xue C, Zhang R, Wu H, Li R, Shen Q (2015) The effect of long-term continuous cropping of black pepper on soil bacterial communities as determined by 454 pyrosequencing. PLoS ONE 10:e0136946. https://doi.org/10.1371/journal.pone.0136946


Yang M, Zhang X, Xu Y, Mei X, Jiang B, Liao J, Yin Z, Zheng J, Zhao Z, Fan L, He X, Zhu Y, Zhu S (2015) Autotoxic ginsenosides in the rhizosphere contribute to the replant failure of Panax notoginseng. PLoS ONE 10:e0118555. https://doi.org/10.1371/journal.pone.0118555


Ye HT, Luo SQ, Yang ZN, Wang YS, Ding Q, Wang KF, Yang SX, Wang Y (2021) Endophytic fungi stimulate the concentration of medicinal secondary metabolites in Houttuynia cordata Thunb. Plant Signal Behav 16(9):1929731. https://doi.org/10.1080/15592324.2021.1929731


Yu J, Zheng Y, Song C, Chen S (2024) New insights into the roles of fungi and bacteria in the development of medicinal plant. J Adv Res. https://doi.org/10.1016/j.jare.2023.12.007


Yuan J, Zhang W, Sun K, Tang MJ, Chen PX, Li X, Dai CC (2019) Comparative transcriptomics and proteomics of Atractylodes lancea in response to endophytic fungus Gilmaniella sp. AL12 reveals regulation in plant metabolism. Front Microbiol. https://doi.org/10.3389/fmicb.2019.01208


Yuan H, Ma Q, Ye L, Piao G (2016) The traditional medicine and modern medicine from natural products. Molecules 21:559. https://doi.org/10.3390/molecules21050559


Zhai X, Luo D, Li X, Han T, Jia M, Kong Z, Ji J, Rahman K, Qin L, Zheng C (2018) Endophyte Chaetomium globosum D38 promotes bioactive constituents accumulation and root production in Salvia miltiorrhiza. Front Microbiol 8:2694. https://doi.org/10.3389/fmicb.2017.02694


Zhang J, Cook J, Nearing JT, Zhang J, Raudonis R, Glick BR, Langille MGI, Cheng Z (2021) Harnessing the plant microbiome to promote the growth of agricultural crops. Microbiol Res 245:126690. https://doi.org/10.1016/j.micres.2020.126690


Zhang C, Ma X, Zhu R, Liu Z, Gu M, Zhang J, Li Y, Xu Y, Zhu D (2020) Analysis of the endophytic bacteria community structure and function of Panax notoginseng based on high-throughput sequencing. Curr Microbiol 77:2745. https://doi.org/10.1007/s00284-020-02068-2


Zhong C, Chen C, Gao X, Tan C, Bai H, Ning K (2022) Multi-omics profiling reveals comprehensive microbe–plant–metabolite regulation patterns for medicinal plant Glycyrrhiza uralensis Fisch. Plant Biotechnol J 20:1874


Zhou JY, Li X, Zhao D, Deng-Wang MY, Dai CC (2016) Reactive oxygen species and hormone signaling cascades in endophytic bacterium induced essential oil accumulation in Atractylodes lancea. Planta 244(3):699–712. https://doi.org/10.1007/s00425-016-2536-0

 


Author Information


Directorate of Medicinal and Aromatic Plants Research, Anand, India