A Multifaceted Exploration of Plant-Microbe Interactions

Plants host diverse ecological niches that foster the growth of numerous microorganisms — bacteria, fungi, and viruses—forming the intricate plant microbiome1. These microbial communities establish complex relationships with plants, engaging in diverse plant activities and bolstering environmental stress resilience2. Today, we're excited to briefly delve into the microbial types and the role of metabolites in shaping plant-microbe interactions.



Plant-microbial interactions3


Microbial Diversity in Plant Interactions

Microbial types span plant rhizosphere, endophytic microbes in roots, above-ground endophytes, and phyllosphere, each wielding varied influences on plants. Beneficial microbial allies like rhizobia, mycorrhizal fungi, endophytes, and epiphytes play pivotal roles. Rhizobia4 and mycorrhizal fungi5 aid nitrogen fixation in legumes and non-legumes, vital for protein synthesis and plant growth. Endophytes synthesize active compounds within plants1, while epiphytes support normal growth under heavy metal stress6. Prompted by these allies, plants produce VOCs (volatile organic compounds) fortifying resistance to stressors7 and enhancing the release of plant volatiles8.


Amid these interactions, plants also grapple with harmful microbes causing severe diseases like phytophthora infestans in potatoes, tobacco mosaic virus, and puccinia striiformis in wheat. However, certain harmful microbes are pivotal for establishing plant root microbiota.


Microbial Diversity in Plants

Plant species


Presence site



Arabidopsis thaliana

Enterobacter sp. SA187

root endophytic

Participate in sulfur metabolism and improve the salt tolerance



Amycolatopsis, Penicillium,



lower absolute abundance of R. solanacearum



Pseudomonas fluorescens PDS1,

Bacillus subtilis KA9


efficiency against Ralstonia solanacearum





negative interaction with Cd content


Salix atrocinerea

Pantoea sp. AV62,

Rhodococcus erythropolis AV96

root endophyte

resulted in higher As and Pb concentrations in both roots and leaves



Plant Metabolites Influencing Plant-Microbe Dynamics

Plant metabolomics profoundly influence rhizospheric microbial composition through root secretions, influenced by plant genotype and domestication. Rhizospheric microbes vary among different plant genotypes due to distinct substances in root exudates—sugars, amino acids, organic acids, nucleotides, fatty acids, hormones, and secondary metabolites. These exudates intricately modulate rhizospheric nutrient effectiveness.


Plant metabolites influencing rhizospheric microbial composition

Plant species





Salix myrtillacea

Azotobacter, Pseudomonas

Fraxetin, sinapyl aldehyde, glycyl-L-tyrosine, l-glutamine

improve willows drought resistance


Rice and wheat


Malate, citrate, and γ-amino butyric acid

improve plant production


Tea plants

Flavobacterium, Myriangium, Parabacteroides

Eophylline, epigallocatechin gallate

Suppress prevalent fungal pathogens.


Avena barbata


Nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic acid

Provide an attractive direction for rhizosphere microbiome



Streptomyces, Bacillaceae, Burkholderiaceae

Glutamic acid

Glutamic acid directly modulates the microbiome composition



formosus LHL10, Sphingomonas sp

Abscisic acid, salicylic acid and gibberellins

Enhance the production of the endogenous phytohormones



Human Interventions and the Microbial Equilibrium

Human interventions like pesticide application can disrupt the delicate balance of the plant microbiome. For instance, excessive imidacloprid use reduces pepper root microbes, hindering growth and disrupting secondary metabolite synthesis (flavones, phenolic acids, phytohormones19. These complex interactions between plants and microorganisms focus significantly on establishing core microbial communities, crucial in addressing breeding-related concerns.



Unraveling the intricate dance between plants and their microbial allies holds the key to a harmonious future for agriculture. By deciphering the chemical conversation of root exudates and harnessing the power of beneficial microbes, we can cultivate biofertilizers and biopesticides tailored to specific plant needs, breeding crops that thrive in the face of adversity. MetwareBio, at the forefront of this agricultural revolution, empowers researchers and farmers alike with comprehensive metabolomics and microbiome sequencing  services, reach out to get started



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2. Ge J, Li D, Ding J, Xiao X, Liang Y. Microbial coexistence in the rhizosphere and the promotion of plant stress resistance: A review. Environ Res. 2023 Apr 1;222:115298. doi: 10.1016/j.envres.2023.115298

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8. Magalhães DM, Lourenção AL, Bento JMS. Beneath the blooms: Unearthing the effect of rhizospheric bacteria on floral signals and pollinator preferences. Plant Cell Environ. 2023 Nov 23. doi: 10.1111/pce.14771

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10. Kashyap AS, Manzar N, Nebapure SM, Rajawat MVS, Deo MM, Singh JP, Kesharwani AK, Singh RP, Dubey SC, Singh D. Unraveling Microbial Volatile Elicitors Using a Transparent Methodology for Induction of Systemic Resistance and Regulation of Antioxidant Genes at Expression Levels in Chili against Bacterial Wilt Disease. Antioxidants (Basel). 2022 Feb 16;11(2):404. doi: 10.3390/antiox11020404

11. Zheng Z, Li P, Xiong Z, Ma T, Mathivanan K, Praburaman L, Meng D, Yi Z, Ao H, Wang Q, Rang Z, Li J. Integrated network analysis reveals that exogenous cadmium-tolerant endophytic bacteria inhibit cadmium uptake in rice. Chemosphere. 2022 Aug;301:134655. doi: 10.1016/j.chemosphere.2022.134655

12. Navazas A, Mesa V, Thijs S, Fuente-Maqueda F, Vangronsveld J, Peláez AI, Cuypers A, González A. Bacterial inoculant-assisted phytoremediation affects trace element uptake and metabolite content in Salix atrocinerea. Sci Total Environ. 2022 May 10;820:153088. doi: 10.1016/j.scitotenv.2022.153088

13. Kong X, Guo Z, Yao Y, Xia L, Liu R, Song H, Zhang S. Acetic acid alters rhizosphere microbes and metabolic composition to improve willows drought resistance. Sci Total Environ. 2022 Oct 20;844:157132. doi: 10.1016/j.scitotenv.2022.157132

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18. Shaffique S, Hussain S, Kang SM, Imran M, Kwon EH, Khan MA, Lee IJ. Recent progress on the microbial mitigation of heavy metal stress in soybean: overview and implications. Front Plant Sci. 2023 Jun 12;14:1188856. doi: 10.3389/fpls.2023.1188856

19. Li D, Zhou C, Wang S, Hu Z, Xie J, Pan C, Sun R. Imidacloprid-induced stress affects the growth of pepper plants by disrupting rhizosphere-plant microbial and metabolite composition. Sci Total Environ. 2023 Nov 10;898:165395. doi: 10.1016/j.scitotenv.2023.165395



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