Plants never make their chemicals alone. A review published in Discover Life argues that the alkaloids, terpenoids and phenolics long treated as purely plant-made products are in fact shaped at every step by the microbes living on and inside plant tissues. The authors, led by Poonam C. Singh and Aradhana Mishra, pull together evidence that endophytes, rhizobacteria and phyllosphere communities act as a kind of second genome for plants, switching biosynthetic pathways up or down through gene transfer, molecular elicitors, metabolic cross-feeding and hormonal rewiring. The implications stretch from crop protection to the industrial production of anticancer and antimalarial compounds.
Secondary metabolites are the plant kingdom’s chemical toolkit. Unlike primary metabolites such as sugars and amino acids, they are not required for basic survival, but they underpin defense against pathogens and herbivores, signalling between organisms, and protection against ultraviolet radiation and oxidative stress. They are also commercially enormous: phenolics, alkaloids, flavonoids and terpenoids are used in pharmaceuticals, nutraceuticals and agriculture for their antimicrobial and anticancer properties. Their production is not fixed. It responds to pathogens, temperature, light, salinity, drought and heavy metals, and it is governed by complex transcriptional networks in which transcription factors respond to phytohormones and environmental cues.
The review organizes plant secondary metabolism around three biosynthetic frameworks. The shikimic acid pathway converts erythrose-4-phosphate and phosphoenolpyruvate into the aromatic amino acids phenylalanine, tyrosine and tryptophan through seven enzymatic steps ending in chorismate. Phenylalanine then feeds the phenylpropanoid pathway via phenylalanine ammonia-lyase, yielding cinnamic acid and derivatives such as coumarins, lignins, flavonoids and stilbenes. The acetate-malonate pathway assembles acetyl and malonyl CoA into polyketide chains through polyketide synthases, producing stilbenes, simple phenolics and certain flavonoid backbones. The isoprenoid routes, the cytosolic mevalonate pathway and the plastidial methylerythritol phosphate pathway, generate the universal five-carbon building blocks IPP and DMAPP, which prenyltransferases extend into the precursors of mono-, sesqui-, di- and triterpenes.
Where do microbes come in? The review identifies direct mechanisms that operate on these pathways themselves. One is horizontal gene transfer of biosynthetic gene clusters, the co-localized gene sets that encode the enzymes of specialized metabolism. Comparative genomics shows homology or functional analogy between biosynthetic pathways of certain plants and their associated microbes, and endophytic fungi and bacteria can produce the same or similar secondary metabolites as their hosts. Transfer can occur through transformation, transduction and conjugation, and via plasmids, transposons and integrative conjugative elements. Direct movement of genes into plant nuclear DNA appears uncommon, but functional integration, in which microbial biosynthetic genes are expressed within the plant micro-environment, can effectively reshape the plant’s metabolite profile.
A second direct mechanism is elicitation. Microbes secrete microbe-associated molecular patterns and signalling molecules, including lipopolysaccharides and flagellin, that are detected by pattern recognition receptors on plant cell membranes. The perception cascade involves calcium influx, reactive oxygen species generation and MAPK signalling, which activate transcription factors of the WRKY, MYB and bHLH families that control biosynthetic genes in the phenylpropanoid, terpenoid and alkaloid pathways. Bacterial flagellin, recognized by the receptor FLS2, triggers pattern-triggered immunity and subsequent metabolite induction. Microbial volatile organic compounds act at a distance, altering hormonal equilibrium and boosting terpene and flavonoid synthesis. The review notes that elicitor-based technologies are already being explored for mass cultivation of secondary metabolites in tissue culture and bioreactors.
The third direct mechanism is metabolic cross-feeding, in which metabolites produced by one organism serve as substrates or signals for another. In the rhizosphere and endosphere, microbial communities supply precursors such as organic acids and the amino acids tryptophan and phenylalanine that feed directly into flavonoid, alkaloid and terpenoid synthesis. Microbes also contribute enzymes, including oxidoreductases, glycosyltransferases and hydrolases, that chemically transform plant metabolites into products with altered biological activity, stability or solubility. Under some environmental conditions, microbial metabolism appears to redirect plant carbon allocation toward secondary metabolite formation, embedding the plant’s chemistry within a shared metabolic network.
Indirect mechanisms are equally consequential. Plant growth-promoting microorganisms improve nutrient availability, and nutrient supply feeds straight into secondary metabolism. Diazotrophs such as Rhizobium, Azospirillum and Azotobacter fix atmospheric nitrogen into ammonia, increasing the supply of aromatic amino acids needed for phenylpropanoid and alkaloid biosynthesis. Phosphate-solubilizing bacteria and fungi such as Pseudomonas, Bacillus and Aspergillus secrete organic acids and phosphatases that release soluble orthophosphate, accelerating ATP-dependent biosynthesis. Microbial siderophores improve iron uptake, and iron is a required cofactor for cytochrome P450 monooxygenases and phenylalanine ammonia-lyase. Hormonal modulation adds another layer: microbial auxins stimulate root development, jasmonate signalling drives terpenoid, alkaloid and phenolic production, salicylic acid signalling promotes phenolics and pathogenesis-related proteins, and microbial ACC deaminase lowers stress ethylene, easing the growth-defense trade-off.
The case studies are where the review becomes concrete. In Artemisia annua, the source of the antimalarial drug artemisinin, the endophytic bacterium Pseudonocardia sp. YIM 63111 upregulates the genes CYP71AV1 and CPR, raising artemisinin accumulation without inhibiting plant growth. An endophytic consortium of Bacillus subtilis, Bacillus licheniformis, Burkholderia sp. and Acinetobacter pittii upregulated a suite of structural genes and downregulated squalene synthase, and the consortium outperformed individual monocultures. Endophytic fungi including Colletotrichum gloeosporioides, Cochliobolus lunatus, Curvularia pallescens and Acremonium persicum also raised artemisinin content alongside plant biomass. In rice, rhizospheric bacteria recruited by root exudates trigger induced systemic resistance, upregulate phenylalanine ammonia-lyase and push carbon through the shikimate pathway, raising ferulic acid, salicylic acid and p-coumaric acid levels; certain Bacillus strains enhance the antioxidant flavone tricin in grains, and Pseudomonas fluorescens induces lignin deposition that blocks the rice blast fungus.
Tomato tells a similar story. Inoculation with Bacillus subtilis and Pseudomonas strains increases expression of PAL and CHS, accumulating the antioxidants chlorogenic acid, caffeic acid and rutin. PGPRs and arbuscular mycorrhizal fungi upregulate phytoene synthase in the carotenoid pathway. Bacterial endophytes including Rhizobium pusense, Methylophilus flavus and Pseudomonas aeruginosa enhance lycopene content, and treatment with Trichoderma viride microspheres raised lycopene by up to 230 percent, total polyphenols by up to 61 percent and overall antioxidant activity by up to 77 percent in tomato fruits. Phyllosphere microbes elicit terpenes such as beta-phellandrene in leaves, volatile compounds that attract predators of herbivorous pests. The review also highlights endophytes that synthesize drugs outright: Taxomyces andreanae produces the anticancer terpenoid paclitaxel, endophytes of Huperzia serrata produce the anti-Alzheimer alkaloid huperzine A, and Alternaria oxytropis of locoweed produces swainsonine.
The biotechnological horizon the authors sketch runs from microbial bio-elicitors, such as chitosan-assisted induction of stilbene phytoalexins in grapevine and laminarin protection against Botrytis cinerea and Plasmopara viticola, to synthetic microbial communities designed from metagenomic and multi-omics data. SynComs of Bacillus subtilis, Trichoderma harzianum, Trichoderma asperellum and Aspergillus species enhanced pepper growth and reshaped rhizosphere communities, and minimal communities have been constructed that retain genes for iron acquisition, nitrogen fixation and hormone-related metabolism. Integrated metagenomics, transcriptomics, proteomics and metabolomics now allow researchers to link microbial taxa to gene expression, enzyme activity and metabolite output directly. Yet the authors are candid about the limits: disentangling microbial causation from plant endogenous factors remains difficult, multi-species consortia are poorly understood compared with single strains, and scaling laboratory plant-microbe synergies to unpredictable field conditions is a substantial hurdle. Harnessing the plant microbiome as a metabolic regulator, they conclude, could raise crop stress tolerance and the supply of high-value natural products, provided the engineering can survive contact with real soil.
Subject of Research: How plant-associated microbes modulate the biosynthesis of plant secondary metabolites
Article Title: Microbial modulation of secondary metabolites biosynthesis in plants
Article References: Chauhan, P., Verma, P., Bhattacharya, A., Tripathi, A., Singh, P. C., Sharma, S. K., & Mishra, A. (2026). Microbial modulation of secondary metabolites biosynthesis in plants. Discover Life, 56(1), Article 41. https://doi.org/10.1007/s11084-026-09761-5
Image Credits: AI Generated
DOI: 10.1007/s11084-026-09761-5
Keywords: plant microbiome, secondary metabolites, endophytes, rhizobacteria, phyllosphere, horizontal gene transfer, microbial elicitors, SynComs, artemisinin, tomato, rice, biotechnology
News Source: Alan Morgan. (October 29, 2026). Plant Microbes Quietly Engineer the Chemistry of Crops and Medicines. Scienmag.
