Plant talk: Root Exudates

Organic Fertilizer For Agriculture

What are root exudates?

Root exudates, sometimes called plant rhizodeposition products, are organic compounds deposited (or exuded) by plant roots into surrounding substrates. These compounds are produced by plants using energy gained during photosynthesis. This phenomenon has long been recognized as a vital communication system between plants and their microbial communities, especially those within the rhizosphere. In fact, plants use their root exudates to provide a food source for microorganisms in low organic matter hydroponic systems. While plants exude these chemical signals throughout their whole bodies, also called their phyllospheres, here we will focus on below ground root-exudation.

What are root exudates made of?

Plant root exudates can be composed of sugars, amino acids, organic acids, vitamins, tannins, phenolic acids, terpenoids, steroids, tannins, polyacetylenes as well as several other high molecular weight polymers such as tannins. Simply put:

“Simple sugars, protein, and carbohydrates. What is that a recipe for? Cakes and cookies.” -Elaine Ingham, Soil Foodweb, Inc.

So, your plant is dumping cakes and cookies all over its surfaces to feed beneficial microorganisms. These compounds help the microbes grow to high populations and protect plant roots from disease-causing organisms attempting to infiltrate plant defenses. The plant provides food for the microbes, and then microbes can colonize roots and confer benefits to the plant such as nutrient uptake and protection from soilborne pathogens.

For a list of examples of the above compounds, see Table 1 in Dakora & Phillips (2002).

What are some functions that root exuded compounds conduct in the soil?

Sugars: Sugars serve as some of the most important carbon sources available for soil microorganisms. Many forms of sugars provide accessible carbon to soil borne microbes. Sugars are also highly abundant in the environment, as they are the building blocks of all polysaccharides like cellulose and hemi-cellulose - which both give rise and structure to plant cell walls; starches - which function in the plant as food storage tissues; as well as several other organic polymers (Gunina and Kuzyakov, 2015).

Amino Acids: You might have seen our recent blog on the roles amino acids (AAs) conduct in the soil and for plants. As root exudates, these compounds can promote microbial growth and activity, soil fertility, and can bind with micronutrients to make them more available to plants(Adler and Key, 2022).

Organic Acids: A broad class of acids, and similar to AAs above, organic acids play a role in the physiochemical process of mineralization/solubilization of poorly available minerals. Organic acids also contribute to the carbon cycle and can aid plants in detoxification of metals from soils (Dakora et al., 2002). Specifically, some organic acids (nicotinic, shikimic, salicylic, cinnamic, and indole-3-acetic) can serve as the preferred carbon source for certain beneficial rhizosphere bacteria (Pantigoso et al., 2021).

Vitamins: Vitamins like Biotin (Vitamin B7) can help with plants under high pH environments (e.g. carbonate stress) and wild mustard plants were seen to exude this vitamin in high amounts when under carbonate stress (Wang et al., 2020).

Tannins (and other HMW compounds): Tannins, one example of a root exuded high molecular weight compound (HMW), can help plants with nitrogen (N) use efficiency as well as the retention of N in agroecosystem soils (Halvorson et al., 2012).

Why do plants make root exudates?

Root exudation is a primary form of communication of plants with their rhizosphere microbiome, facilitating several responses such as nutrient absorption and competition, plant to plant signaling, and the recruitment of beneficial microorganisms (Canarini et al., 2019).

Plant nutrition: Phenolic acids from root exudates, as one example, are commonly exuded compounds from N-fixing leguminous plants. These phenolics are essential signals to nodule-forming Rhizobiaceae bacteria, and it is in these nodules where atmospheric N is converted to ammonia, a plant-available form of N. Organic acids from root exudates can also convert unavailable forms of Ca-, Fe-, and Al-phosphates into plant usable forms of these nutrients, which is particularly important in field soil systems where large proportions of applied phosphates can be “locked up” by the presence of these calcium, iron, and aluminum ions and unavailable to the plant (Meng et al., 2021). Additionally, plants growing in low-nutrient environments can use root exudates to signal soil microbes to aid in nutrient procurement (Dakora and Phillips, 2002).

Microbial recruitment: Plants change their root exudate patterns to recruit microbes that help accommodate their developmental needs, and these needs change as the plant ages. For example, arabidopsis plants secrete mostly sugars during early growth but as the plant matures, exudation compounds switch from mostly sugars to mostly amino acids and phenolics (Chaparro et al., 2013). It was also demonstrated that applying root exudates from arabidopsis to soils in the absence of plants resulted in presence of highly similar microbiota as observed when arabidopsis plants were growing in those soils (Broeckling et al., 2008). Interestingly, anywhere from 5% to 21% of all photosynthetically fixed carbon is transferred to the rhizosphere in the form of root exudates (Pantigoso et al., 2021).

Exudate re-uptake: Plants can also re-uptake their exudates to prevent wasting of energy. This occurrence is best studied by using radio-labeled isotopic carbon 13 (13C), as this unique form of carbon can be tracked through the plant body and soils in controlled systems. As an example, tomato plants were seen to re-uptake their root exudates when growing in P deficient growing systems (Tiziana et al., 2021).

Beneficial plant-plant signaling: Some plant root exudates can induce defense responses in neighboring plants when the exuding plant is under attack. This can signal to neighboring plants that can respond to the signals to start producing defense compounds to lower their susceptibility to the attacking pathogen. These signals can sometimes tell neighboring plants to initiate production of volatile compounds that attract root shielding microorganisms or insect predators of plant enemies. (Bias et al., 2006).

”Effectively creating a castle wall, protecting the plant…” -Elaine Ingham, Soil Foodweb, Inc.

Detrimental plant-plant signaling: Examples of negative plant to plant communication by root exudates could be resource competition, chemical interference, or parasitism. Allelopathy is one example of chemical interference, and is characterized as when plants directly exude phytotoxins in the soil to limit growth of a close growing, but unrelated plant species. Also, parasitic plants (plants that can’t photosynthesize or produce chlorophyll) such as the ghost plant (Monotropa uniflora) use exudates from their hosts to associate onto their roots (Bias et al., 2006).

How are root exudates collected and studied?

Oftentimes plants are grown in lab systems to study exudates without environmental contamination during collection. But, exudates can also be sampled in soil systems to better understand their ecological roles. After collection, these compounds are studied using laboratory techniques such as Mass Spectrometry. This technique can measure the mass to charge ratio of ions in a mixed sample. Once the mass to charge ratio is known, compounds can be identified and quantified from that sample. For further reading on exudate collection and analysis, see sections 2-3 of Pantigoso et al., (2021).

Why are root exudates important to understand?

These compounds deposited by plants contain a wide variety of molecules released into the soil. These molecules act as signals or messages to allow communication between plant roots to other plant roots as well as soil microorganisms. They influence several plant factors from nutrient uptake, to attracting microorganisms that shield plant roots and help keep phytopathogens in balance within the soil microbial community. The complexity of plant root exudates lies on the extensive variability in composition, quality, and quantity of compounds that vary among plant species, genotypes, and environmental conditions [9]. More than 100,000 plant secondary metabolites have been identified, and a large fraction of them are encompassed in the form of root exudates [52]. Therefore, a combination of techniques is required for analyzing such diverse metabolites expressing different polarities and molecular weight ranges [53].

What role do root exudates play in my cultivation system?

Keeping in mind everything we have covered, it should be clear that the rhizosphere is a highly dynamic and diverse place. While we cannot control plant root exudation, growers should be aware of it and learn to use exudation advantageously. One instance of utilizing root exudate might look like the application of beneficial microbes in low-organic matter (limited microbe food) systems, such as hydroponics. It is commonly thought that a carbon source (e.g. molasses) should be applied in tandem with plant-growth promoting rhizobacteria (PGPRs) in these systems to provide them with food. While often true for most PGPRs, phytopathogens can also utilize molasses for growth, such as members of the Fusarium genus (Xie et al., 2013). So, while adding a microbe food can help, know that plants in your system are already providing for their root microbiota in the form of root exudation.

“If the plant was putting out food that attracted a disease-causing organism, the plant would be dead” -Elaine Ingham, Soil foodweb, Inc. 

Thanks for reading "Plant talk: Root Exudates". This piece was written by: Michael J. DiLegge, MSc Director of Microbiology at Impello Biosciences. 

 For further reading on root exudates see the references used to write this blog:

1. Adler L, Key M. Amino Acids in Agriculture. (2022);

2. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM. The role of root exudates in rhizosphere interactions with plants and other diversity. Appl Environ Microbiol. (2008); 74(3):738-44. doi: 10.1128/AEM.02188-07. Epub 2007 Dec 14. PMID: 18083870; PMCID: PMC2227741.

3. Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM. Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol. (2008); 74(3):738-44. doi: 10.1128/AEM.02188-07. Epub 2007 Dec 14. PMID: 18083870; PMCID: PMC2227741.

4. Canarini A., Kaiser C., Merchant A., Richter A., Wanek W. Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli Front. Plant Sci. (2019); 21

5. Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM. Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions. PLoS ONE (2013); 8(2): e55731.

6. Dakora, F.D., Phillips, D.A. Root exudates as mediators of mineral acquisition in low-nutrient environments. Plant and Soil (2002); 245, 35–47.

7. Garcia, D. K., Chapela, I. H., Chadwick, O. A., Hansen, M. W., Herren, H. R., Hillel, D., Ingham, E., ... Lily Films,. (2012). Symphony of the soil.

8. Gunina A, Kuzyakov Y., Sugars in soils and sweets for microorganisms: Review or origin, content, composition and fate Soil biol. & Biochem. (2015);

9. Halvorson J., Gonzales J., Hagerman E., Changes in Soluble-N in Forest and Pasture Soils after Repeated Applications of Tannins and Related Phenolic Compounds. Int’l Jol of Agronomy (2012);

10. Meng X, Chen W, Wang Y, Huang Z, Ye X, Chen L, Yang L. Effects of phosphorus deficiency on the absorption of mineral nutrients, photosynthetic system performance and antioxidant metabolism in Citrus grandis. PLoS One (2021).

11. Pantigoso HA, He Y, DiLegge MJ, Vivanco JM. Methods for Root Exudate Collection and Analysis. Methods Mol Biol. (2021); 2232:291-303. doi: 10.1007/978-1-0716-1040-4_22. PMID: 33161555.

12. Tiziana R., Fabio T., Toury P., Silva C., Stefano C.,Tanja M. Tomato plants reuptake root exudates and alter carbon isotope fractionation under phosphorus deficiency. (2021); vEGU21, the 23rd EGU General Assembly, held online 19-30 April, 2021,id.EGU21-9459

13. Wang Y., Wang M., Ye X., Liu H., Takano T., Tsugama D., Liu S., Bu Y., Biotin plays an important role in Arabidopsis thaliana seedlings under carbonate stress. Plant Science (2020); 300, Xie J, Song L, Li X, Wu Q, Wang C, Zu H, Cao Y, Qiao D. Isolation and identification of oleaginous endophytic fungi. (2013) African Jol. of Microbiol. Research. Vol.7(19) p. 2014-2019


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