2.3. QS—A Messenger in Rhizosphere
Plant-growth promoting and biocontrol bacteria, such as certain
Pseudomonas biocontrol strains, are affected by QS systems as well. Biosynthesis of antibiotics and other antifungal compounds, such as phenazines, pyrrolnitrin, 2,4-diacetylphloroglucinol, hydrogen cyanide and pyoluteorin, are related to the
phzIR QS system in
Pseudomonas aureofaciens [
118] and the
pcoIR system in
Pseudomonas fluorescens [
119], among others. Researchers have shown that the QS system
pcoIR in
P. fluorescens 2P24 controls the biocontrol activity of this agent by indirectly regulating the production of several metabolites, including 2,4-diacetylphloroglucinol, hydrogen cyanide, siderophores and proteinases that are important for its biocontrol capacity; this is in contrast to the
phzIR QS system in
P. aereofaciens 30–84, which is used to positively regulate the
phzFABCD operon responsible for synthesizing phenazine [
120].
Quorum sensing was also found to modulate expression of virulence genes in
P. aeruginosa, a plant pathogen that infects the roots of
Arabidopsis and sweet basil. Walker
et al. [
121] traced plant infection and subsequent mortality due to
P. aeruginosa strains PAO1 and PA14 to the formation of biofilm colonies at the root surface, which were dependent on the QS system. Two AHL-mediated quorum sensing circuits have been identified in
P. aeruginosa. The
lasIR system has been shown to regulate expression of several virulence factors, including extracellular enzymes and toxins, and the
rhlIR system is involved in modulating the expression of several of the virulence factors also controlled by the
las system [
50]. In contrast, the
lasIR and
rhlIR QS systems in the plant growth-promoting bacteria
P. aeruginosa strain PUPa3 are involved in establishing beneficial associations with plants. These systems are important for rhizosphere colonization and act in concert to effect virulence toward
Caenorhabditis elegans and the wax moth [
122].
A study by Müller,
et al. [
123] demonstrated that AHL-mediated QS is also crucial for biocontrol activity of
Serratia plymuthica HRO-C48, a ubiquitous inhabitant of the rhizosphere of different plant species that plays an antagonistic role to many soil-borne pathogens. The influence of AHL-mediated communication in this bacterial strain includes production of extracellular proteolytic and chitinolytic enzymes, synthesis of volatile organic compounds (VOCs) and pyrrolnitrin (which is involved in antifungal activity), and upregulation of the plant growth hormone indole-3-acetic acid.
Functional bacterial genes are expressed only when bacterial populations have reached a critical number, with either pathogenic or beneficial consequences to the host. Therefore, bacteria use quorum sensing to ensure the optimal time to activate plant responses, in order to avoid premature defense [
124]. The transgenic tobacco plant was used to expression gene
expI of
Erwinia carotovora, the soft-rot phytopathogen, which is responsible for
N-oxoacyl-homoserine lactone (OHL) biosynthesis. The synthesis of OHL in tobacco exhibited enhanced resistance to infection by wild-type
E. carotovora and exogenous addition of OHL to wild-type tobacco also had a similar result [
124]. The results from experiments by Toth
et al. [
125] showed that transgenic potato plants containing the gene encoding AHL synthase from
Yersinia enterocolitica increased disease development by infection with
E. carotovora. These results suggest that the regulation of plant cell wall-degrading enzymes by AHLs is likely a response to increased nutrient availability at later stages of infection.
Recently, this specific behavior of bacteria has also been described for fungi in the control of important processes such as biofilm formation and pathogenesis [
126]. The signaling molecules, farnesol, tyrosol, dimethoxycinnamate and trisporic acid, produced by
Candida albicans,
Uromyces phaseoli and zygomycetes, are involved in microbe-host interactions [
126]. However, there is also evidence that signals from bacteria and fungi interrelate and interact with one another. The QS signaling molecule 3-oxo-C12-HSL from
P. aeruginosa inhibits the transition from yeast-form to filamentous growth in
C. albicans, which is linked to virulence [
51]. In turn, farnesol is able to strongly suppress AHL synthesis in
P. aeruginosa [
127]. However, the molecular pathways and the precise mechanisms of action in fungal QS systems remain unknown [
126]. A study by Uroz and Heinonsalo [
128] showed the potential for mycorrhizal or non-mycorrhizal root-associated fungi to degrade AHL or to prevent AHL recognition by producing quorum sensing inhibitors (QSI). This phenomenon could be a strategy developed by fungi to interfere with the deleterious bacterial functions and to control bacterial community behavior in or near plant roots.
Signaling molecules are crucial substances that coordinate the expression of certain genes and influence the activity of microbial strains within the rhizosphere. However, it is interesting that these microbial signals and sophisticated information feedback systems can be detected by and responded to by plant roots. The results from Mathesius
et al. [
129] indicate that the eukaryotic host
M. truncatula is able to detect nanomolar to micromolar concentrations of bacterial AHLs from both symbiotic and pathogenic bacteria; the corresponding functional responses to AHLs were significantly affected, including changes in auxin balance and flavonoid synthesis proteins, as well as the secretion of plant compounds. Surprisingly, Schuhegger
et al. [
130] showed that AHLs within the rhizosphere produced by
Serratia liquefaciens and
Pseudomonas putida which colonized tomato roots, increased systemic resistance to the fungal leaf pathogen
Alternaria alternata in tomato shoots. Studies in which roots were inoculated with different types of AHLs show that short chain AHLs (e.g., C4-HSL and C6-HSL) increase
Arabidopsis root length by altering plant hormone concentrations in root and shoot tissues, while the accumulation of long chain AHLs in root tissues appears to reduce root growth [
131]. Therefore, the response of plants to AHLs depends on various external factors, such as AHL type and concentration. Plants or parts of the plant will react differently to treatment with AHLs, although the mechanisms of transport and the identity of the receptor for these signaling molecules in plants are almost completely unknown.
It is possible that higher plants may also synthesize and secrete compounds that mimic the activity of bacterial AHL signaling compounds. The AHL signal-mimic activities detected in pea (
Pisum sativum) exudates might play important roles in stimulating AHL-regulated behaviors in certain bacterial strains while inhibiting these behaviors in others [
132]. This suggests that there is significant crosstalk between different bacterial species and plant roots within the rhizosphere, which is mediated through precise combinations of signal transduction and response regulation. Structures of most AHL signal-mimic compounds have not been elucidated; however, earlier findings reported that secondary metabolites from algae had structural similarities to AHL molecules [
133]. Considering the inhibition of microbial growth by secondary metabolites from plants, the fact that bacterial quorum sensing systems are affected by these compounds is not surprising.
l-Canavanine, an arginine analog produced by alfalfa or other legumes, inhibited AHL-signaling processes in the reporter strain
Chromobacterium violaceum without interfering with its growth. In addition,
l-cananavine appeared to regulate
S. meliloti quorum sensing system responsible for the regulation of EPS II biosynthesis [
134].
2.4. Other Features of Roots Exudates
Plant roots are the key source of energy or food for living organisms, so the region of soil that surrounds the root has the potential to promote the chemotaxis of soil microbes by root exudates [
20]. Large quantities of organic compounds are released at the surface of roots, such as sugars, polysaccharides, amino acids, phenolic, polyacetylenes, flavonoids, fatty acids, growth regulators, nucleotides, tannins, steroids, terpenoids, alkaloids, and vitamins [
20]. Researchers have tested the effects of root exudates on patterns of bacterial gene expression. Mark
et al. [
135] examined the influence of exudates from two varieties of sugar beet on the
Pseudomonas aeruginosa transcriptome and showed that the exudates selected for genetically distinct
Pseudomonas spp. populations within the rhizosphere. Their results showed that the majority of genes were regulated in response to only one of the two exudates. Interestingly, genes with altered expression included those with functions previously implicated in microbe-plant interactions, with effects on metabolism, chemotaxis and type III secretion. Root exudates have the potential to impact rhizosphere microbes both positively and negatively. For example, studies of chemotaxis behavior in pathogenic microbes, such as
Ralstonia solanacearum, showed that these microorganisms depend on root exudates to locate and infect plant hosts in their natural niches [
136]. The root exudates can also serve as signals between parasitic plants and host plants. These active compounds, such as haustorium inducing factors (HIFs) and 2,6-dimethoxy-1,4-benzoquinone (DMBQ), influence both germination and haustorium stage of parasitic plants [
137].
In some sense, root exudates are highly plant species-specific, and they influence specific microbial communities [
5]. However, these compounds secreted by plants have also shown versatility under complex below-ground conditions. For example, the nodulation genes of nitrogen-fixing bacteria are induced by flavones and isoflavones, which are beneficial for leguminous plants, while zoospores of
Phytophthora sojae, a soybean pathogen, are specifically attracted to isoflavones for host recognition and infection initiation [
138]. Flavonoids have various functions within the rhizosphere with respect to the interaction of roots with microorganisms, including chemoattraction, stimulating rhizobial
nod gene expression, mycorrhizal spore germination, and inhibiting root pathogens (as mentioned above), as well as chelating soil nutrients, affecting quorum sensing, and mediating allelopathic interactions between plants [
56,
139,
140].
Recent review summarized some flavonoids involved in allelopathic inhibitor of seedling growth, such as 5,7,4′-trihydroxy-3′,5′-dimethoxyflavone, quercetin and kaempferol [
140]. Plant roots secrete allelochemicals as phytotoxins, which mainly exert their influence through resource competition and inhibition of germination and seedling growth in neighboring plants. These detrimental interactions are also described as plant defenses in response to stress or local rhizosphere conditions [
141]. Allelochemicals from bigalta limpograss (
Hemarthria altissima) root are mainly phenolic compounds that serve as plant growth inhibitors [
142]. These phenolic compounds were analyzed by gas chromatography-mass spectrometry and were found to contain 3-hydroxyhydrocinnamic, benzoic, phenylacetic, and hydrocinnamic acids, which are major rhizospheric compounds with known growth-regulatory activities. The effects of root exudates on ion uptake by cucumber seedlings were examined using phenolic acids, such as cinnamic acid, vanillic acid, and ferulic acid. Among the compounds tested,
o-hydroxybenzoic acid showed the strongest effect on nutrient absorption in cucumber [
143].