Plant Metabolomics in Plant–Microbe Interactions

Plant metabolomics, through systematic analysis of metabolites produced by plants and microorganisms, reveals the complex chemical dialogue mechanisms between them. These metabolites not only mediate the establishment of symbiotic relationships but also play a role in plant defense processes against pathogens.

Metabolites: The Chemical Language of Plants and Microorganisms

Metabolites secreted by plant roots are key factors in shaping the rhizosphere microbial community. These metabolites mainly include secondary metabolites such as flavonoids, strigolactones, coumarins, and triterpenoids. They can act as signaling molecules, nutrient sources, or antibacterial substances, selectively promoting the growth of beneficial microorganisms and inhibiting the reproduction of harmful microorganisms.

For example, citric acid secreted by cucumber roots can attract Bacillus belyssus SQR9 and promote its biofilm formation; fumaric acid secreted by banana roots has a similar attraction and promoting effect on Bacillus subtilis N11. Flavones are another critical class of root exudates; they can induce the expression of bacterial nodulation genes and initiate the formation of root nodules.

Diagram showing possible sites of interactions between plants and microbiota (Gupta S et al., 2022)

Metabolomics Technologies Aid in Elucidating Interaction Mechanisms

Advanced metabolomics technologies provide powerful tools for elucidating plant-microbe interactions. The application of ultra-high performance liquid chromatography-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) enabled researchers to detect 71 mycorrhizal metabolites in alfalfa arbuscular mycorrhizal symbiotic roots, with these metabolites present in concentrations more than 10 times higher in mycorrhizal roots than in uninoculated roots.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MSI) provides spatial location information of metabolites. A study on alfalfa root nodules detected the distribution of various amino acids, organic acids, sugars, lipids, and flavonoids, and obtained molecular ion images of nitrogen-fixing and non-nitrogen-fixing nodules.

Metabolomics analysis flow for plant–microbe interaction research (Gupta S et al., 2022)

Metabolomics Reveals Specific Interaction Mechanisms

Studies have shown that plant-microbe interactions are particular.

• Baker NR et al. used LC-MS/MS non-targeted metabolomics technology, combined with 16S rRNA microbial sequencing, to construct a rhizosphere metabolite-microbe association network. They discovered a specific response of the rhizosphere metabolite profile to nitrogen (N) nutrients:
  • Under nitrogen-limited (nitrogen deficiency) stress, the roots of Sedum aizoon significantly enrich and secrete a specific set of metabolites, mainly including aromatic acids (such as chlorogenic acid and cinnamic acid), pentoses and their derivatives (such as glucuronic acid).
  • Conversely, under nitrogen-sufficient conditions, the rhizosphere is enriched with nitrogen-rich compounds, such as serotonin and tetrahydrothiazole (ectoine).
  • The study also found that the accumulation of aromatic acids and other metabolites under nitrogen-deficient conditions was positively correlated with increased abundance of bacterial groups such as Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. These microorganisms may be adept at utilizing these compounds as sources of carbon and energy.
  • Under nitrogen-sufficient conditions, the accumulation of nitrogen-rich metabolites (such as serotonin) coincided with the proliferation of faster-growing Actinobacteria.
• Beneficial microorganisms, such as rhizosphere bacteria and fungi, can promote plant growth and health by regulating plant metabolism.
  • Metabolomics analysis reveals that beneficial microorganisms can influence plant physiological states by synthesizing or regulating key plant hormones. For example, microbial-produced giberrelin, auxin, and cytokinin converge with plant biosynthetic pathways to jointly restrict growth and development. More importantly, microorganisms can degrade the ethylene precursor ACC, reducing ethylene levels in plants under stress and thus alleviating the inhibitory effects of stress on growth.
  • Studies have found that quorum sensing signaling molecules such as acylhomoserine lactones produced by rhizosphere microorganisms can be recognized by plants as cross-species signals, thereby regulating gene expression and metabolism and enhancing stress resistance. This indicates that microbial metabolites are an essential language in the plant-microorganism "chemical dialogue."
  • Under stresses such as drought and high temperature, important stress-resistance compounds such as phenols and flavonoids accumulate significantly in plants inoculated with beneficial microorganisms. Metabolomics data confirm that changes in these metabolites are closely related to the plant's enhanced antioxidant defense system, providing direct evidence that microorganisms help plants alleviate stress damage.

Climate-induced stress and metabolite-plant-microbe interaction (Olanrewaju OS et al., 2024)

• Narasimhan K et al. combined targeted and non-targeted rhizomics methods, utilizing reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (RP-HPLC-ESI/MS), to discover that plants and microorganisms play distinct and interdependent roles, jointly forming a highly efficient rhizosphere bioremediation team:
  • Targeted Recruitment: Plants (such as wild-type Arabidopsis thaliana) actively secrete particular secondary metabolites through their roots, primarily phenylpropanoid compounds (such as flavonoids). These metabolites act as precise "job postings" and "food" to the rhizosphere environment.
  • Creating Nutrient Preferreds: These metabolites provide a growth advantage for specific microorganisms that can utilize them as nutrient sources, selectively enriching these beneficial bacteria in the rhizosphere and shaping specific microbial communities.
  • Functional Execution: The recruited specific microorganisms (such as Pp-wt strains that can utilize phenylpropanoids) are not only "diners" of the plant but also executors of its functions. They possess the ability to degrade pollutants (such as polychlorinated biphenyls, PCBs).
  • Competitive Advantage: Because they can exclusively utilize the exceptional "food" (flavonoids, etc.) provided by plants, these functional organisms have a 100-fold higher colonization capacity in the rhizosphere than strains that cannot utilize these substances, ensuring their population dominance and effectiveness.
  • The combination of the two produces a powerful "1+1>2" effect. Plants support specific microorganisms by secreting metabolites, while the microorganisms "repay" the plant by degrading contaminants, creating a cleaner growing environment. In the experiment, the team removed 90% of the pollutants within two weeks, significantly outperforming the effects of either working alone.
• Thoenen L et al. used LC-MS for high-throughput, precise qualitative and quantitative analysis, identifying key metabolic events through comparative analysis, and finally confirming the structures of key metabolites using NMR and other techniques.
  • Metabolomics analysis determined that benzoxazine compounds secreted by maize roots, especially its main component MBOA, are specific metabolite signals used by maize to select its root microorganisms.
  • Bacteria carrying the bxdA gene (such as Microbacterium and Sphingomonas) can exclusively utilize MBOA, an exceptional "food" provided by maize roots, thus gaining a significant colonization advantage in the rhizosphere (accumulating approximately 7.7% in the maize rhizosphere). In contrast, such bacteria are very rare in the rhizosphere of plants that do not produce benzoxazine (such as Arabidopsis) or plants with low levels of MBOA in their root exudates (such as certain wheat varieties).
• Jia Y et al. used GC-MS non-targeted metabolomics to compare and analyze lightly aromatic (LAT) and intensely aromatic (SAT) tobacco leaves. Metabolomics revealed key metabolite differences and microorganisms determining their aroma quality:
  • Lightly aromatic (LAT) tobacco: Marked by significantly higher levels of carbohydrate metabolites (such as sucrose and maltose). These sugars contribute to a milder aroma and reduce harshness.
  • Strontly aromatic (SAT) tobacco: Marked by higher levels of organic acids and amino acids (such as xylinum acetic acid, tartaric acid, and L-glutamic acid).
  • Microorganisms enriched in LAT (such as Methylobacterium and Pseudomonas) were positively correlated with higher levels of carbohydrate metabolites.
  • Microorganisms enriched in SAT (such as Methylobacterium and Sphingosporium) were positively correlated with higher levels of acids and amino acid metabolites.
  • A notable finding is that Alkalococcus may have a "bidirectional regulatory" effect on aroma metabolites, revealing the complexity of the microbial regulatory network of plant metabolism.

Untargeted metabolomics data of tobacco from GC-MS (Jia Y et al., 2025)

Decoding Plant-Microbe Interactions: Current Challenges and Future Pathways

Research into plant-microbe chemical relationships continues to advance rapidly. This field holds significant promise for developing sustainable agricultural solutions and novel pharmaceutical approaches. Understanding these complex interactions requires sophisticated analytical methods and innovative research strategies.

Current Research Challenges

Scientists face several technical hurdles in studying these chemical exchanges:

• Precisely capturing root-released compounds without contamination
• Distinguishing whether metabolites originate from plants or microbes
• Processing complex chemical data from mixed biological systems

Future Research Directions

Next-generation studies will leverage integrated multi-omics approaches:

• Combining transcriptomic, metabolic, and microbial community data
• Applying high-resolution mass spectrometry and spatial imaging
• Developing computational models to predict interaction outcomes

These advanced techniques will help researchers understand the complete chemical conversation between plants and their microbial partners.

Practical Applications and Industry Impact

The knowledge gained from these studies directly benefits multiple sectors:

• Agricultural companies developing targeted microbial fertilizers
• Pharmaceutical researchers discovering new plant-derived compounds
• Biotechnology firms engineering enhanced plant-microbe systems

As analytical technologies continue evolving, we will uncover more profound insights into nature's chemical communication networks. These discoveries will drive the next generation of sustainable agricultural and pharmaceutical innovations.

To understand untargeted metabolomics in plant research, you can refer to "Untargeted Metabolomics in Plant Research: Opportunities and Challenges".

People Also Ask

Is metabolomics an emerging tool to study plant-microbe interactions?

In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses.

What are the applications of metabolomics in plants?

Metabolomics enables us to improve genetically modified plants, and helps us to estimate associated risks by allowing us to get a glimpse of their complex biochemistry viainformative snapshots acquired at different time points during plant development.

What is the biggest benefit of metabolomics?

One of the major strengths of metabolomics is its ability to provide a real-time, dynamic snapshot of metabolic changes in response to disease, treatment, or lifestyle alterations.

What are the limitations of metabolomics?

The most challenging part of a metabolomic study is confirmation of biomarker identity. This is an essential step toward understand the biological changes occurring within the system and remains a major bottleneck in metabolomics investigations.

Is metabolomics an emerging tool for the study of plant pathogen interactions?

Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant–microbe interaction.

How many cells do you need for metabolomics?

How much sample do I need for metabolomic profiling? Minimum amount of material required: Cell culture: 1-2 million cells. Microbial pellet: 5-25 mg.

What is metabolomics in plant disease management?

Worldwide crop output and monetary losses are caused by plant diseases, which continue to be major challenges to agricultural productivity. The goal of metabolomics is to quickly and efficiently analyze intricate combinations of metabolites in order to identify and measure each and every metabolite.

What is metabolomics in plant disease management?

Worldwide crop output and monetary losses are caused by plant diseases, which continue to be major challenges to agricultural productivity. The goal of metabolomics is to quickly and efficiently analyze intricate combinations of metabolites in order to identify and measure each and every metabolite.

References

1. Mhlongo MI, Piater LA, Madala NE, Labuschagne N, Dubery IA. The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance. Front Plant Sci. 2018 Feb 9;9:112.
2. Gupta S, Schillaci M, Roessner U. Metabolomics as an emerging tool to study plant-microbe interactions. Emerg Top Life Sci. 2022 Apr 15;6(2):175-183.
3. Baker NR, Zhalnina K, Yuan M, Herman D, Ceja-Navarro JA, Sasse J, Jordan JS, Bowen BP, Wu L, Fossum C, Chew A, Fu Y, Saha M, Zhou J, Pett-Ridge J, Northen TR, Firestone MK. Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes. Proc Natl Acad Sci U S A. 2024 Aug 6;121(32):e2303439121.
4. Olanrewaju OS, Glick BR, Babalola OO. Metabolomics-guided utilization of beneficial microbes for climate-resilient crops. Curr Opin Chem Biol. 2024 Apr;79:102427.
5. Narasimhan K, Basheer C, Bajic VB, Swarup S. Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol. 2003 May;132(1):146-53.
6. Thoenen L, Kreuzer M, Pestalozzi C, Florean M, Mateo P, Züst T, Wei A, Giroud C, Rouyer L, Gfeller V, Notter MD, Knoch E, Hapfelmeier S, Becker C, Schandry N, Robert CAM, Köllner TG, Bruggmann R, Erb M, Schlaeppi K. The lactonase BxdA mediates metabolic specialisation of maize root bacteria to benzoxazinoids. Nat Commun. 2024 Aug 2;15(1):6535.
7. Jia Y, Wang J, Lin X, Liang T, Dai H, Wu B, Yang M, Zhang Y, Li R. Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves. Front Plant Sci. 2025 Jun 3;16:1588888.