This slide describes root exudates and its function in plant-microbe interaction

1. Root exudates: Functions in
plant-microbe interactions
Debayan Nandi
M.Sc student
Dept. of Biotechnology
Prepared by

2. Root exudates
 Root exudates, are chemicals exuded by the
roots of growing plants.
 They are readily available to micro-
organisms and are of great importance for the
population of the plant root surfaces.
 Root exudation includes the secretion of
ions, free oxygen and water, enzymes,
mucilage, and a diverse array of carbon-
containing primary and secondary metabolites.
Definition
Fig. Release of root exudates in
the rhizosphere
Root
Root border
cells

3. Introduction
 Roots are integral to a plant’s growth and survival; and secrete an
enormous range of compounds into the surrounding soil
 Root secretes to compete with the invading root systems of neighboring
plant species and with soil-borne microorganisms, including bacteria,
fungi, and insects
 The compounds secreted are referred as root exudates and serve
important roles as chemical attractants and repellants in the rhizosphere,
the narrow zone of soil that surrounds the root system
 Studying the root system of the model plant Arabidopsis thaliana (L.)
has been indispensable in advancing our understanding of the impact of
agricultural practices on root development and the impact of roots

4. Root exudates
Through the exudation of a wide variety of compounds
1. Roots may regulate the soil microbial community.
2. Encourage beneficial symbioses.
3. Change the chemical and physical properties of the soil .
4. Inhibit the growth of competing plant species .
5. 5% to 21% of all photosynthetically fixed carbon being
transferred to the rhizosphere through root exudates
Functions

5. Components of root exudates
Root exudates
Low molecular weight exudates High molecular weight exudates
Organic acid
Amino acids
Sugar
Phenolics
Protein
Polysaccharide

6. Fig.1. Carbon flow in plants- carbon dioxide is assimilated by plants and used for
synthesis of metabolites and release root exudates; its various components to influence
soil properties and residing microbiota (Musilova, Ridl et al. 2016).

7. Root interactions
2. Root-root Communication
 Allelopathy is mediated by the release of certain secondary metabolites
by plant roots and plays an important role in the establishment and
maintenance of terrestrial plant communities.
 parasitic plants often use secondary metabolites secreted from roots as
chemical messengers to initiate the development of invasive organs
(haustoria) required for heterotrophic growth
 A secondary metabolite secreted by the roots of knapweed (Centaurea
maculosa) provides a classic example of root exudates exhibiting negative
root-root communication in the rhizosphere.

8. 2. Root-Microbe Communication
 roots have been shown to play an important role in root microbe
interactions include flavanoids present in the root exudates of legumes
that activate Rhizobium meliloti genes responsible for the nodulation
process (Peters et al., 1986)
 Erwinia spp., Pseudomonas spp., and Agrobacterium spp., possess
quorum-sensing systems that control the expression of several genes
required for pathogenicity
 Root exudates from pea (Pisum sativum) seedlings were found to
contain several bioactive components that mimicked AHL signals in
well-characterized bacterial reporter strains, stimulating AHL-regulated
behaviors in some strains against pathogenicity

9. Factors affecting exudates
1. Microorganisms
 In rhizosphere, the roots have to compete with the microorganisms in
their vicinity for water, nutrients, space that mainly includes fungi and
bacteria and insects feeding on an abundant source of organic material
 Root exudates acts as messengers in physical and biological
interaction with the other plant roots and microorganisms and also
encourages beneficial symbioses inhibit growth of pathogenic microbes
 The rate of exudation or exudates formation is increased by the
presence of microbes in the rhizosphere (Matilla et al. 2010)

10. 2. Soil pH and fertilizers
 High concentrations of anions and organic acids in root exudation lead
to P deficiency and this lowers rhizospheric pH, making Mn, Fe and Zn to
be more available in calcareous soils
 As micronutrients such as Mn, Fe and Al occur in high concentrations
below pH (5.5) hence rhizospheric acidification below pH 5.5 can cause
some major macronutrients to become limiting
 However, organic acids from root exudates are able to solubilize
unavailable soil Ca, Fe and Al phosphates
Rooibos tea (Aspalathus linearis L.) can actively modify their
mycorhizospheric pH by extruding OH- and HCO3
- to facilitate growth in
low pH soils (pH usually between 3 to 5) (Dakora and Phillips, 2002)

11. 3. Plant characteristics (species, age, nutrients, light)
 Plant age alters the rhizosphere microorganism and the stage of plant
maturity controls the magnitude of rhizosphere effect and degree of
response to specific microorganisms
 Some microbes were found to be more effective at the time of
flowering than in the seedling or full maturity stage
 The effect of light on the production of pectin and polygalacturonase
(PG) in the root exudates of Trifolium alexandrinum inoculated with an
efficient strain of Rhizobium trifolii was investigated. The pectin methyl
esterase PME and PG increased with an increase in the duration of light to
which plants were exposed (Chhonkar, 1978).

12. Mechanism of root exudation
Fig.2. Mechanism of root exudation of compounds through the plant cell membrane PM =
Plasma Membrane; TMD = Transmembrane Domain; NBD = Nucleotide Binding Domain
(Bertin, Yang et al. 2003)

13. Rhizosphere microbes influence plant root exudation
 Studies reported that the colonization of arbuscular mycorrhizal fungi
influences plant root exudation, e.g., increasing secretions of nitrogen,
plant phenolics, gibberellins and reducing secretions of sugars, potassium
ions, and phosphorus
A. thaliana was found to produce distinct root exudation profiles when
cultured with Pseudomonas putida KT2440 (Matilla et al. 2010).
 soil bacterium Achromobacter piechaudi ARV8 that has ACC
deaminase activity was able to increase tomato and pepper seedling
biomass (Mayak et al. 2004)

14. Secondary metabolites and hormones
 plants produce and release numerous secondary metabolites and
hormones into the rhizosphere, many of which play a role in plant–
microbe interactions.
benzoxazinoids, found in the root exudates of maize, attract plant-
beneficial rhizobacteria
Pseudomonas species contain chemotaxis sensory proteins for amino
acids that aid in their colonization of tomato roots
 presence of PGPR B. Subtilis invokes abscisic acid and salicylic acid
signaling pathways in A. thaliana, resulting in the closure of stomata
and the restriction of pathogen entry (Kumar et al. 2012)

15. Plant-microbe interaction mediated by root exudates
Plant –microbe interaction
Positive plant-microbe interactions Negative plant-microbe interactions
Plant growth
promoting bacteria
(PGPB)
Root nodulation
Mycorrhizal associations
Antimicrobial effects

16. Fig.2. Representation of the complex interactions mediated by root exudates that take place
in the rhizosphere between plant roots and other organisms (Walker, Bais et al. 2003).

17. Fig. Schematic representation of possible rhizospheric interactions mediated
by root exudates. (Bais et al. 2006)

18. Alteration in the characteristics of soil by root exudation
 A large range of organic and inorganic substances are secreted by roots
into the soil, that leads to changes in its biochemical and physical
properties (Rougier 1981).
 It has been speculated that as the soil dries, exudates begin to lose
water to soil, its viscosity increases and hence the resistance to movement
of soil particles in contact with exudates will increase. (McCully and
Boyer 1997).
 Plants have also been found more hydrated in the early morning hours
compared with the midday samplings (McCully and Boyer 1997).

19.  This approach to visualizes root development on the observed
interface to access the 3D structure of a root system
Methods for the study of interaction between root and
associated microorganisms
 Tracing of exuded compounds, including their uptake by rhizosphere
microflora, can be studied through fluorescence-based methods.
 In the past, biosensors have been developed for studying carbon flow
through plant exudates (Porteous, Killham et al. 2000), during nodulation,
and for tracing bacterial quorum sensing and root colonization.

20. Object of study Method
Root growth and morphology
Observation windows + imaging system
Transparent culture media, e.g.,
PhytagelTM or NafionTM
Computed Tomography (CT)
Magnetic Resonance Imaging (MRI)
Neutron radiography
Plant–microbe interaction
(tracing of exuded compounds, carbon
flow in exudates)
Biosensors
Fluorescence in situ hybridization
Metagenomics
Table.1. An overview of methods for studying roots and root exudates and their
interaction with microbe in the rhizosphere. (Musilova, Ridl et al. 2016).

21. Fig. Differentiation of border root cells alongwith the secretion of root exudates
(Musilova, Ridl et al. 2016)

22. Conclusion
Various technological advancements and research over the past few years
facilitated a better understanding of root exudates and such advancements
can be applied in agriculture to achieve a good yield and increase in
productivity by mediating defensive responses against various soil-borne
pathogens and can be applied for developing better methods to deal with
invading crops, heavy metals and various toxic compounds. Future
challenges mainly includes the absolute characterization of different
chemical compounds of root exudates that exhibits resistance to diseases
and facilitate more beneficial association with plants and microorganisms
present in the rhizosphere.

23. References
 Jones DL Darrah PR (1994). Role of root derived organic acids in the
mobilization of nutrients from the rhizosphere. Plant Soil. 166:247-257.
 Bais HP, Prithiviraj B, Jha AK, Ausubel FM, Vivanco JM (2005)
Mediation of pathogen resistance by exudation of antimicrobials
from roots. Nature 434:217–221.
 Chet I, Ordentlich A, Shapira R, Oppenheim A (1990) Mecahnisms of
biocontrol of soil-borne plant pathogens by rhizobacteria. Plant
Soil 129:85–92
 Doornbos RF, Van Loon LC, Bakker PAHM (2009) Beneficial
Pseudomonas spp. have altered root colonization on Arabidopsis
thaliana mutants affected in the expression of induced systemic
resistance. IOBC/WPRS Bull 43:307–310

24.  Musilova, L., et al. (2016). "Effects of secondary plant metabolites
on microbial populations: Changes in community structure and
metabolic activity in contaminated environments." International journal
of molecular sciences 17(8): 1205.
 Porteous, F., et al. (2000). "Use of a lux-marked rhizobacterium as a
biosensor to assess changes in rhizosphere C flow due to pollutant
stress." Chemosphere 41(10): 1549-1554.
 Rougier, M. (1981). Secretory activity of the root cap. Plant
Carbohydrates II, Springer: 542-574.