Effect of transporters on the secretion of phytochemicals by the roots of Arabidopsis thaliana

Effects of ρ-hydroxybenzoic acid on metabolism and excretion of grapevine root

Autotoxicity is a significant contributor to replant disease, with phenolic acid autotoxins such as 4-HBA (ρ-hydroxybenzoic acid) influencing the structure of the rhizosphere microbial community by modifying the secretion characteristics of grapevine roots. In the study, 'Beta' grape seedlings were selected to investigate the regulatory mechanism of 4HBA on root metabolism and secreting characteristics. The results showed that the expression level of genes related to primary and secondary metabolism in the roots was affected by 100 μg mL-1 4-HBA treatment, and the genes related to starch and sucrose metabolism were generally down-regulated, and most genes encoding glycolytic pathway, amino acid pathway and phenylpropanoid biological pathway were up-regulated. A total of 142 metabolites were significantly changed after 100 μg mL-1 4-HBA treatment, of which 92 metabolites were significantly up-regulated and 50 metabolites were significantly down-regulated. 7 amino acids, 3 phenolic acids, 2 nucleotides, 2 flavonoids, 4 organic acids, and 9 fatty acids might be regulated by ABC transporter. Further research found that some metabolites regulated by ABC transporter affected the growth of Fusarium solani, a harmful fungus related to grape replant disease. Our research confirmed that 4-HBA not only alters root metabolism but also modifies the content of root exudates, among which ABC transporters playing a crucial role in the efflux process.

Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana

Background

Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions.

Methods

Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions.

Results

Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software.

Conclusions

The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

High aquaporin expression correlates with increased translocation of quinclorac from shoots to roots in resistant Echinochloa crus-galli var. zelayensis

BACKGROUND

Echinochloa crus-galli var. zelayensis is a troublesome weed in rice fields and can be controlled by using quinclorac. However, over-reliance on quinclorac has resulted in resistant (R) barnyardgrass, which differs significantly in its ability to transport quinclorac compared to susceptible (S) barnyardgrass. This study aimed to investigate the underlying mechanisms for this different translocation between R and S barnyardgrass.

RESULTS

Larger amount of quinclorac was transferred from shoots to roots in R compared to S barnyardgrass. After 1 day of quinclorac [300 g active ingredient (a.i.) ha^-1 ] foliar treatment, its content in shoots of R was 81.92% of that in S barnyardgrass; correspondingly, in roots of R was 1.17 fold of that in S barnyardgrass. RNA-sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the expression levels of PIPs belonging to aquaporins (AQPs) in R were higher than in S barnyardgrass, with or without quinclorac treatment. With co-application of quinclorac and AQPs inhibitors [mercury(II) chloride (HgCl₂ )] treatment, even though the expression levels of PIPs and the transport rates of quinclorac were both suppressed in R and S barnyardgrass, this process was less pronounced in R than in S barnyardgrass.

CONCLUSION

This report provides clear evidence that higher PIPs expression results in rapid quinclorac translocation from shoots to roots and reduces the quinclorac accumulation in the shoot meristems in R barnyardgrass, thus reducing the control efficacy of quinclorac. © 2022 Society of Chemical Industry.

Root exudates contribute to belowground ecosystem hotspots: A review

Root exudates are an essential carrier for material cycling, energy exchange, and information transfer between the belowground parts of plants and the soil. We synthesize current properties and regulators of root exudates and their role in the belowground ecosystem as substances cycle and signal regulation. We discussed the composition and amount of root exudates and their production mechanism, indicating that plant species, growth stage, environmental factors, and microorganisms are primary influence factors. The specific mechanisms by which root secretions mobilize the soil nutrients were summarized. First, plants improve the nutrient status of the soil by releasing organic acids for acidification and chelation. Then, root exudates accelerated the SOC turnover due to their dual impacts, forming and destabilizing aggregates and MASOC. Eventually, root exudates mediate the plant-plant interaction and plant-microbe interaction. Additionally, a summary of the current collection methods of root exudates is presented.

Characterizing rhizosphere microbial communities associated with tolerance to aboveground herbivory in wild and domesticated tomatoes

Root-associated microbial communities are well known for their ability to prime and augment plant defenses that reduce herbivore survival or alter behavior (i.e., resistance). In contrast, the role root microbes play in plant tolerance to herbivory, an evolutionarily sustainable alternative to resistance, is overlooked. In this study, we aimed to expand our limited understanding of what role rhizosphere microbial communities play in supporting tolerance to insect damage. Using domesticated tomatoes and their wild ancestors (Solanum spp.), we first documented how tobacco hornworm (Manduca sexta) herbivory impacted tomato fruit production in order to quantify plant tolerance. We then characterized the bacterial and fungal rhizosphere communities harbored by high and low tolerance plants. Wild tomatoes excelled at tolerating hornworm herbivory, experiencing no significant yield loss despite 50% leaf area removal. Their domesticated counterparts, on the other hand, suffered 26% yield losses under hornworm herbivory, indicating low tolerance. Ontogeny (i.e., mid- vs. late-season sampling) explained the most variation in rhizosphere community structure, with tomato line, tolerance, and domestication status also shaping rhizosphere communities. Fungal and bacterial community traits that associated with the high tolerance line include (1) high species richness, (2) relatively stable community composition under herbivory, and (3) the relative abundance of taxa belonging to Stenotrophomonas, Sphingobacterium, and Sphingomonas. Characterizing tolerance-associating microbiomes may open new avenues through which plant defenses are amended in pest management, such as plant breeding efforts that enhance crop recruitment of beneficial microbiomes.

Dissection of grasspea (Lathyrus sativus L.) root exoproteome reveals critical insights and novel proteins

The plant exoproteome is crucial because its constituents greatly influence plant phenotype by regulating physiological characteristics to adapt to environmental stresses. The root exudates constitute a dynamic aspect of plant exoproteome, as its molecular composition ensures a beneficial rhizosphere in a species-specific manner. We investigated the root exoproteome of grasspea, a stress-resilient pulse and identified 2861 non-redundant proteins, belonging to a myriad of functional classes, including root development, rhizosphere augmentation as well as defense functions against soil-borne pathogens. Significantly, we identified 1986 novel exoproteome constituents of grasspea, potentially involved in cell-to-cell communication and root meristem maintenance, among other critical roles. Sequence-based comparison revealed that grasspea shares less than 30 % of its exoproteome with the reports so far from model plants as well as crop species. Further, the exoproteome revealed 65 % proteins to be extracellular in nature and of these, 37 % constituents were predicted to follow unconventional protein secretion (UPS) mode. We validated the UPS for four stress-responsive proteins, which were otherwise predicted to follow classical protein secretion (CPS). Conclusively, we recognized not only the highest number of root exudate proteins, but also pinpointed novel signatures of dicot root exoproteome.

Shoot base responds to root-applied glutathione and functions as a critical region to inhibit cadmium translocation from the roots to shoots in oilseed rape (Brassica napus)

Glutathione (GSH) is a tripeptide involved in controlling heavy metal movement in plants. Our previous study showed that GSH, when site-specifically applied to plant roots, inhibits Cd translocation from the roots to shoots in hydroponically cultured oilseed rape (Brassica napus) plants. A factor that led to this inhibitory effect was the activation of Cd efflux from root cells. To further investigate the molecular mechanism triggered by root-applied GSH, Cd movement was non-invasively monitored using a positron-emitting tracer imaging system. The Cd absorption and efflux process in the roots were visualized successfully. The effects of GSH on Cd efflux from root cells were estimated by analyzing imaging data. Reanalysis of image data suggested that GSH applied to roots, at the shoot base, activated Cd return. Cutting the shoot base significantly inhibited Cd efflux from root cells. These experimental results demonstrate that the shoot base plays an important role in distributing Cd throughout the plant body. Furthermore, microarray analysis revealed that about 400 genes in the roots responded to root-applied GSH. Among these, there were genes for transporter proteins related to heavy metal movement in plants and proteins involved in the structure modification of cell walls.

Enhancing the 1-Aminocyclopropane-1-Carboxylate Metabolic Rate of Pseudomonas sp. UW4 Intensifies Chemotactic Rhizocompetence

1-aminocyclopropane-1-carboxylic acid (ACC) is a strong metabolism-dependent chemoattractant for the plant beneficial rhizobacterium Pseudomonas sp. UW4. It is unknown whether enhancing the metabolic rate of ACC can intensify the chemotaxis activity towards ACC and rhizocompetence. In this study, we selected four promoters to transcribe the UW4 ACC deaminase (AcdS) gene in the UW4 ΔAcdS mutant. PA is the UW4 AcdS gene promoter, PB20, PB10 and PB1 are synthetic promoters. The order of the AcdS gene expression level and AcdS activity of the four strains harboring the promoters were PB20 > PA > PB10 > PB1. Interestingly, the AcdS activity of the four strains and their parent strain UW4 was significantly positively correlated with their chemotactic activity towards ACC, rhizosphere colonization, roots elongation and dry weight promotion. The results released that enhancing the AcdS activity of PGPRenable them to achieve strong chemotactic responses to ACC, rhizocompetence and plant growth promotion.

1-Aminocyclopropane-1-Carboxylate: A Novel and Strong Chemoattractant for the Plant Beneficial Rhizobacterium Pseudomonas putida UW4

Plant growth-promoting rhizobacteria (PGPR) and fungi-bacterial biofilms are both important biofertilizer inoculants for sustainable agriculture. However, the strongest chemoattractant for bacteria to colonize the rhizosphere and mycelia is not clear. Coincidentally, almost all the PGPRs possess 1-aminocyclopropane-1-carboxylate (ACC) deaminase (AcdS) and can utilize ACC as the sole nitrogen source. Here, we found that ACC was a novel, metabolic dependent and methyl-accepting chemoreceptor-involved chemoattractant for Pseudomonas putida UW4. The chemotactic response of UW4 to ACC is significantly greater than that to the amino acids and organic acids identified in the plant root and fungal hyphal exudates. The colonization counts of the UW4 acdS or cheR deletion mutants in the wheat rhizosphere and on Agaricus bisporus mycelia were reduced one magnitude compared with those of UW4. The colonization counts of UW4 on A. bisporus antisense ACC oxidase mycelia with a high ACC production significantly increased compared with A. bisporus, followed by the UW4 cheR complementary strain and the ethylene chemoreceptor gene-deletion mutant. The colonization counts of the UW4 strains on A. bisporus acdS⁺ mycelia with a low ACC production decreased significantly compared with A. bisporus wild type. These results suggested that ACC and not ethylene should be the strongest chemoattractant for the PGPR that contain AcdS.

Plant Root Exudates Are Involved in Bacillus cereus AR156 Mediated Biocontrol Against Ralstonia solanacearum

The biological control process mediated by microbes relies on multiple interactions among plants, pathogens and biocontrol agents (BCAs). One such efficient BCA is Bacillus cereus AR156, a bacterial strain that controls a broad spectrum of plant diseases and potentially works as a microbe elicitor of plant immune reactions. It remains unclear, however, whether the interaction between plants and B. cereus AR156 may facilitate composition changes of plant root exudates and whether these changes directly affect the growth of both plant pathogens and B. cereus AR156 itself. Here, we addressed these questions by analyzing the influences of root exudate changes mediated by B. cereus AR156 during biocontrol against tomato bacterial wilt caused by Ralstonia solanacearum. Indeed, some upregulated metabolites in tomato root exudates induced by B. cereus AR156 (REB), such as lactic acid and hexanoic acid, induced the growth and motile ability of in vitro B. cereus AR156 cells. Exogenously applying hexanoic acid and lactic acid to tomato plants showed positive biocontrol efficacy (46.6 and 39.36%) against tomato bacterial wilt, compared with 51.02% by B. cereus AR156 itself. Furthermore, fructose, lactic acid, sucrose and threonine at specific concentrations stimulated the biofilm formation of B. cereus AR156 in Luria-Bertan- Glycerol- Magnesium medium (LBGM), and we also detected more colonized cells of B. cereus AR156 on the tomato root surface after adding these four compounds to the system. These observations suggest that the ability of B. cereus AR156 to induce some specific components in plant root exudates was probably involved in further biocontrol processes.

Chemical signaling involved in plant-microbe interactions

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

Phenolic chemistry of the seagrass Zostera noltei Hornem. Part 1: First evidence of three infraspecific flavonoid chemotypes in three distinctive geographical regions

The flavonoid content of Zostera noltei leaves was investigated over a broad spatial scale using chromatographic and spectroscopic techniques (HPLC-DAD, LC/MS and NMR). Samples were collected at fifteen localities covering Mediterranean Sea and NE Atlantic coast, and representative of three types of coastal ecosystems: mesotidal bays, coastal lagoons, and open-sea. Three geographically distinct flavonoid chemotypes were identified on the basis of their respective major compound. One is characterized by apigenin 7-sulfate (Eastern part of Gulf of Cadiz), one by diosmetin 7-sulfate (French Atlantic coast and Mediterranean Sea), and the third contained similar quantities of the above two compounds (Mauritania and South Portugal). Our results show that metabolomic profiling using a combination of analytical techniques is a tool of choice to characterize chemical phenotype accurately. This work emphasizes for the first time the spatial variability in the flavonoid chemistry of Z. noltei throughout Atlantic and Mediterranean range, and constitutes the first report of chemical races in the Zosteraceae family. This infraspecific chemical differentiation should be considered when dealing with the role of Z. noltei in coastal ecosystems or in the selection of the best population donor for Z. noltei beds restoration. Combined with molecular identification, phenolic fingerprinting might be helpful to elucidate the evolutionary history of Z. noltei.

Arabidopsis Transporter ABCG37/PDR9 contributes primarily highly oxygenated Coumarins to Root Exudation

The chemical composition of root exudates strongly impacts the interactions of plants with microorganisms in the rhizosphere and the efficiency of nutrient acquisition. Exudation of metabolites is in part mediated by ATP-binding cassette (ABC) transporters. In order to assess the contribution of individual ABC transporters to root exudation, we performed an LC-MS based non-targeted metabolite profiling of semi-polar metabolites accumulating in root exudates of Arabidopsis thaliana plants and mutants deficient in the expression of ABCG36 (PDR8/PEN3), ABCG37 (PDR9) or both transporters. Comparison of the metabolite profiles indicated distinct roles for each ABC transporter in root exudation. Thymidine exudation could be attributed to ABCG36 function, whereas coumarin exudation was strongly reduced only in ABCG37 deficient plants. However, coumarin exudation was compromised in abcg37 mutants only with respect to certain metabolites of this substance class. The specificity of ABCG37 for individual coumarins was further verified by a targeted LC-MS based coumarin profiling method. The response to iron deficiency, which is known to strongly induce coumarin exudation, was also investigated. In either treatment, the distribution of individual coumarins between roots and exudates in the investigated genotypes suggested the involvement of ABCG37 in the exudation specifically of highly oxygenated rather than monohydroxylated coumarins.

Root exudates: the hidden part of plant defense

The significance of root exudates as belowground defense substances has long been underestimated, presumably due to being buried out of sight. Nevertheless, this chapter of root biology has been progressively addressed within the past decade through the characterization of novel constitutively secreted and inducible phytochemicals that directly repel, inhibit, or kill pathogenic microorganisms in the rhizosphere. In addition, the complex transport machinery involved in their export has been considerably unraveled. It has become evident that the profile of defense root exudates is not only diverse in its composition, but also strikingly dynamic. In this review, we discuss current knowledge of the nature and regulation of root-secreted defense compounds and the role of transport proteins in modulating their release.

Managing heavy metal toxicity stress in plants: biological and biotechnological tools

The maintenance of ion homeostasis in plant cells is a fundamental physiological requirement for sustainable plant growth, development and production. Plants exposed to high concentrations of heavy metals must respond in order to avoid the deleterious effects of heavy metal toxicity at the structural, physiological and molecular levels. Plant strategies for coping with heavy metal toxicity are genotype-specific and, at least to some extent, modulated by environmental conditions. There is considerable interest in the mechanisms underpinning plant metal tolerance, a complex process that enables plants to survive metal ion stress and adapt to maintain growth and development without exhibiting symptoms of toxicity. This review briefly summarizes some recent cell biological, molecular and proteomic findings concerning the responses of plant roots to heavy metal ions in the rhizosphere, metal ion-induced reactions at the cell wall-plasma membrane interface, and various aspects of heavy metal ion uptake and transport in plants via membrane transporters. The molecular and genetic approaches that are discussed are analyzed in the context of their potential practical applications in biotechnological approaches for engineering increased heavy metal tolerance in crops and other useful plants.

Transcriptome analysis of Arabidopsis thaliana plants in response to kin and stranger recognition

Recent reports have demonstrated that Arabidopsis thaliana has the ability to alter its growth differentially when grown in the presence of secretions from other A. thaliana plants that are kin or strangers, however, little knowledge has been gained as to the physiological processes involved in these plant-plant interactions. Therefore, we examined the root transcriptome of A. thaliana plants exposed to stranger versus kin secretions to determine genes involved in these processes. We conducted a whole transcriptome analysis on root tissues and categorized genes with significant changes in expression. Genes from four categories of interest based on significant changes in expression were identified as ATP/GST transporter, auxin/auxin related, secondary metabolite and pathogen response genes. Multiple genes in each category were tested and results indicated that pathogen response genes were involved in the kin recognition response. Plants were then infected with Pseudomonas syringe pv. Tomato DC3000 to further examine the role of these genes in plants exposed to own, kin and stranger secretions in pathogen resistance. This study concluded that multiple physiological pathways are involved in the kin recognition. The possible implication of this study opens up a new dialogue in terms of how plant-plant interactions change under a biotic stress.

Root exudates mediate kin recognition in plants

Though recent work has demonstrated that plants can recognize species, kin versus strangers, and self/non-self roots, no mechanism for identity recognition in plants has yet been found. Here we examined the role of soluble chemicals in signaling among roots. Utilizing Arabidopsis thaliana, we exposed young seedlings to liquid media containing exudates from siblings, strangers (non-siblings), or only their own exudates. In one experiment, root secretions were inhibited by sodium orthovanadate and root length and number of lateral roots were measured. In a second experiment, responses to siblings, strangers, and their own exudates were measured for several accessions (genotypes), and the traits of length of the longest lateral root and hypocotyl length were also measured. The exposure of plants to the root exudates of strangers induced greater lateral root formation than exposure of plants to sibling exudates. Stranger recognition was abolished upon treatment with the secretion inhibitor. In one experiment, plants exposed to sibling or stranger exudates have shorter roots than plants only exposed to their own exudates. This self/non-self recognition response was not affected by the secretion inhibitor. The results demonstrate that that kin recognition and self/non-self are two separate identity recognition systems involving soluble chemicals. Kin recognition requires active secretion by roots.

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

This review evaluates the importance of root exudates in determining rhizosphere bacterial community structure. We present evidence that indicates that: (1) the direct influence of root exudates on rhizosphere bacterial communities is limited to small spatiotemporal windows related to root apices; (2) upon rapid assimilation by microorganisms, root exudates are modified, independent of plant influences, before rerelease into the rhizosphere by the microorganisms themselves--thus, at short distances from root apices, rhizosphere carbon pools are unlikely to be dominated by root exudates; and (3) many of the major compounds found in root exudates are ubiquitous in the rhizosphere as they are found in other pools of rhizodeposits and in microbial exudates. Following this argument, we suggest that the importance of root exudates in structuring rhizosphere bacterial communities needs to be considered in the context of the wider contribution of other rhizosphere carbon pools. Finally, we discuss the implications of rhizosphere bacterial distribution trends for the development of effective strategies to manage beneficial plant-microorganism interactions.

Root secretion of phytochemicals in Arabidopsis is predominantly not influenced by diurnal rhythms

Root-secreted phytochemicals mediate multiple interactions in the rhizosphere. The root exudation process can be altered by various biotic factors, including pathogenic and non-pathogenic microbes, and abiotic factors like temperature and soil moisture. It has been suggested that root secretion of specific flavonoids is influenced by diurnal rhythms (by light or dark) but a comprehensive analysis of the overall secretion of phytochemicals in response to diurnal rhythms has not been studied. In this study, we analyzed the effect of light/dark cycles on root exudation profiles using Arabidopsis as a model plant. Our results reveal that the root secretion of phytochemicals is partly regulated by the diurnal light cycle and follows two main patterns of secretion: (1) the large majority of phytochemicals in the exudates showed no diurnal pattern in their secretion, and (2) a few compounds showed a diurnal pattern in their secretion: three compounds increased in secretion only under light; two compounds increased in secretion only while it was dark; and two compounds increased in secretion during the transition from dark to light. Root-specific ABC transporters have been implicated in root exudation; an analysis of the gene expression patterns of ABC transporters in the roots of Arabidopsis at specific time points revealed that none of the ABC transporters followed a diurnal expression pattern, suggesting that they are expressed constantly during the day and night. Similarly, we analyzed the expression in roots of genes involved in secondary metabolite biosynthesis and found that some of the genes involved in phenylpropanoid and glucosinolate biosynthesis (i.e. 4-coumarate-CoA ligases (4CL1 and 4CL2), flavonol synthases (FS1 and FS2), and CYP79B3) followed distinct diurnal expression patterns. Overall, we have discovered that while root exudation of the majority of phytochemicals is constitutive, the secretion of a few compounds follows a diurnal rhythm, which is in accordance with the expression of some genes involved in secondary metabolism.

Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere

The rhizosphere is strongly influenced by plant-derived phytochemicals exuded by roots and plant species exert a major selective force for bacteria colonizing the root-soil interface. We have previously shown that rhizobacterial recruitment is tightly regulated by plant genetics, by showing that natural variants of Arabidopsis thaliana support genotype-specific rhizobacterial communities while also releasing a unique blend of exudates at six weeks post-germination. To further understand how exudate release is controlled by plants, changes in rhizobacterial assemblages of two Arabidopsis accessions, Cvi and Ler where monitored throughout the plants' life cycle. Denaturing gradient gel electrophoresis (DGGE) fingerprints revealed that bacterial communities respond to plant derived factors immediately upon germination in an accession-specific manner. Rhizobacterial succession progresses differently in the two accessions in a reproducible manner. However, as plants age, rhizobacterial and control bulk soil communities converge, indicative of an attenuated rhizosphere effect, which coincides with the expected slow down in the active release of root exudates as plants reach the end of their life cycle. These data strongly suggest that exudation changes during plant development are highly genotype-specific, possibly reflecting the unique, local co-evolutionary communication processes that developed between Arabidopsis accessions and their indigenous microbiota.

Regulation and function of root exudates

Root-secreted chemicals mediate multi-partite interactions in the rhizosphere, where plant roots continually respond to and alter their immediate environment. Increasing evidence suggests that root exudates initiate and modulate dialogue between roots and soil microbes. For example, root exudates serve as signals that initiate symbiosis with rhizobia and mycorrhizal fungi. In addition, root exudates maintain and support a highly specific diversity of microbes in the rhizosphere of a given particular plant species, thus suggesting a close evolutionary link. In this review, we focus mainly on compiling the information available on the regulation and mechanisms of root exudation processes, and provide some ideas related to the evolutionary role of root exudates in shaping soil microbial communities.

Transcriptional profiling of the PDR gene family in rice roots in response to plant growth regulators, redox perturbations and weak organic acid stresses

The role of plant pleiotropic drug resistance (PDR) type ATP-binding cassette (ABC) transporters remains poorly understood. We characterized the expression of the rice pleiotropic drug resistance (PDR) gene family in roots, where PDR transporters are believed to have major functions. A prototypical oligonucleotide array was developed containing 70-mers chosen in the gene-specific 3' untranslated regions of the rice PDR genes, other full-molecule rice ABC transporter genes and relevant marker genes. Jasmonates, which are involved in plant defense and secondary metabolism, proved major inducers of PDR gene expression. Over half of the PDR genes were JA-induced in roots of rice; OsPDR9 to the highest level. Salicylic acid, involved in plant pathogen defense, markedly induced the expression of OsPDR20. OsPDR20 was cDNA cloned and characterized. Abscisic acid, typically involved in water deficit responses, particularly induced OsPDR3 in roots and shoot and OsPDR6 in rice leaves. OsPDR9 and OsPDR20 were furthermore up-regulated in response to dithiothreitol- or glutathione-induced redox perturbations. Exogenous application of the weak organic acids lactic acid, malic acid, and citric acid differentially induced the expression of OsPDR3, OsPDR8, OsPDR9 and OsPDR20 in rice seedling roots. This transcriptional survey represents a guide for the further functional analysis of individual PDR transporters in roots of rice.

Differential secretion and accumulation of terpene indole alkaloids in hairy roots of Catharanthus roseus treated with methyl jasmonate

The induction of several secondary metabolites in plants is one of the most commonly observed effects after the external addition of methyl jasmonate (MeJA). After the elicitation of Catharanthus roseus hairy roots with different concentrations of MeJA, changes in the accumulation of alkaloids such as ajmalicine, serpentine, ajmaline and catharanthine were observed. In addition to the increased accumulation of alkaloids in the tissues, the root exudation of phytochemicals increased compared to that of the non-treated control hairy roots. Moreover, MeJA induced differential secretion of several C. roseus hairy root metabolites.

Root exudates regulate soil fungal community composition and diversity

Plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. A few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. This study demonstrates that two model plant species (Arabidopsis thaliana and Medicago truncatula) are able to maintain resident soil fungal populations but unable to maintain nonresident soil fungal populations. This is mediated largely through root exudates: the effects of adding in vitro-generated root exudates to the soil fungal community were qualitatively and quantitatively similar to the results observed for plants grown in those same soils. This effect is observed for total fungal biomass, phylotype diversity, and overall community similarity to the starting community. Nonresident plants and root exudates influenced the fungal community by both positively and negatively impacting the relative abundance of individual phylotypes. A net increase in fungal biomass was observed when nonresident root exudates were added to resident plant treatments, suggesting that increases in specific carbon substrates and/or signaling compounds support an increased soil fungal population load. This study establishes root exudates as a mechanism through which a plant is able to regulate soil fungal community composition.

Transcriptome analysis of Arabidopsis roots treated with signaling compounds: a focus on signal transduction, metabolic regulation and secretion

Gene expression in response to signaling molecules has been well studied in the leaves of the model plant species Arabidopsis thaliana. However, knowledge of gene expression and metabolic regulation at the root level is limited. Here, the signaling compounds salicylic acid (SA), methyl jasmonate (MeJA) and nitric oxide (NO) were applied exogenously to induce various defense responses in roots, and their effect was studied using a combination of genomic, molecular and biochemical approaches. Genes involved in defense signaling/activation, cellular redox state, metabolism, transcription factors and membrane transport were altered in expression following treatment with SA, MeJA and NO. In addition, it was found that SA-, MeJA- and NO-elicited roots increased the root exudation of phytochemicals compared with the roots of nontreated control plants. Transport systems likely to be involved in the root exudation of phytochemicals, including the MATE, ABC, MFS, amino acid, sugar and inorganic solute transporters, showed altered expression profiles in response to treatments. Overall, significant differences were found in the signaling compound-elicited expression profiles of genes in roots vs those in leaves. These differences could be correlated to the underground nature of roots and their exposure to higher microbial inoculum rates under natural conditions.

Small molecule approaches in plants

Small molecules offer exciting opportunities for plant science. So far, bioactive small molecules have been identified as plant hormones, herbicides, growth regulators, or taken from animal research. Recently, plant scientists have started to explore further the chemical space for novel modulators of plant hormone signalling, and have followed up this work with exciting discoveries illustrating the potential of small molecules such as brassinazole and sirtinol. New chemical genetic screens have been designed to generate chemical tools for the investigation of membrane trafficking, gravitropism and plant immunity. Further novel 'chemetic' tools to identify targets and modes of action are currently generated through an intimate interdisciplinary collaboration between biologists and small molecule chemists.