Secretion dynamics of soyasaponins in soybean roots and effects to modify the bacterial composition

Soyasaponins are triterpenoid saponins widely found in legume plants. These compounds have drawn considerable attention because they have various activities beneficial for human health, and their biosynthesis has been actively studied. In our previous study, we found that legume plants including soybean secrete soyasaponins from the roots in hydroponic culture throughout the growth period, but the physiological roles of soyasaponins in the rhizosphere and their fate in soil after exudation have remained unknown. This study demonstrates that soyasaponins are secreted from the roots of field-grown soybean, and soyasaponin Bb is the major soyasaponin detected in the rhizosphere. In vitro analysis of the distribution coefficient suggested that soyasaponin Bb can diffuse over longer distances in the soil in comparison with daidzein, which is a typical isoflavone secreted from soybean roots. The degradation rate of soyasaponin Bb in soil was slightly faster than that of daidzein, whereas no soyasaponin Bb degradation was observed in autoclaved soil, suggesting that microbes utilize soyasaponins in the rhizosphere. Bacterial community composition was clearly influenced by soyasaponin Bb, and potential plant growth-promoting rhizobacteria such as Novosphingobium were significantly enriched in both soyasaponin Bb-treated soil and the soybean rhizosphere. These results strongly suggest that soyasaponin Bb plays an important role in the enrichment of certain microbes in the soybean rhizosphere

Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions

Growth- and health-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is such a bacterium that efficiently colonizes roots, modifies the architecture of the root system to increase its size, and induces systemic resistance to make plants more resistant to pests and pathogens. Our previous work suggested that WCS417-induced phenotypes are controlled by root cell-type-specific mechanisms. However, it remains unclear how WCS417 affects these mechanisms. In this study, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. We found that the cortex and endodermis have the most differentially expressed genes, even though they are not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, and mutant analysis suggests that this downregulation facilitates WCS417-driven root architectural changes. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis of WCS417-colonized roots. Using an endodermal barrier mutant, we showed the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Comparison of the transcriptome profiles in the two epidermal cell types that are in direct contact with WCS417—trichoblasts that form root hairs and atrichoblasts that do not—implies a difference in potential for defense gene activation. While both cell types respond to WCS417, trichoblasts displayed both higher basal and WCS417-dependent activation of defense-related genes compared with atrichoblasts. This suggests that root hairs may activate root immunity, a hypothesis that is supported by differential immune responses in root hair mutants. Taken together, these results highlight the strength of cell-type-specific transcriptional profiling to uncover “masked” biological mechanisms underlying beneficial plant-microbe associations

Cell-type specific transcriptomics reveals roles for root hairs and endodermal barriers in interaction with beneficial rhizobacterium

Growth-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is a well-studied bacterium that promotes growth of many plant species. Upon colonization, WCS417 affects root system architecture resulting in an expanded root system. Both immunity and root system architecture, are controlled by root-cell-type specific biological mechanisms, but it is unknown how WCS417 affects these mechanisms. Therefore, here, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. The cortex and endodermis displayed the most differentially expressed genes, even though they were not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, possibly facilitating the root architectural changes observed in WCS417-colonized roots. Comparison of the transcriptome profiles in the two epidermal cell types that were in direct contact with WCS417 -- trichoblasts that form root hairs and atrichoblasts that do not -- imply functional specialization. Whereas basal expression levels of nutrient uptake-related genes and defense-related genes are highest in trichoblasts and atrichoblasts, respectively, upon exposure to WCS417 these roles revert. This suggests that root hairs participate in the activation of root immunity, further supported by attenuation of immunity in a root hairless mutant. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis in WCS417-colonized roots. Using an endodermal barrier mutant we show the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Altogether, we highlight the strength of cell-type-specific transcriptional profiling to uncover masked biological mechanisms underlying successful plant-microbe associations

Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen‐fixing rhizobial symbiosis

Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad‐spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen‐associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae‐specific PRR ELONGATION FACTOR‐THERMO UNSTABLE RECEPTOR (EFR), conferring recognition of the bacterial EF‐Tu protein, from Arabidopsis thaliana to the legume Medicago truncatula. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF‐Tu‐derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR‐Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling

Crying out for help with root exudates : adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes

Plants employ immunological and ecological strategies to resist biotic stress. Recent evidence suggests that plants adapt to biotic stress by changing their root exudation chemistry to assemble health-promoting microbiomes. This so-called ‘cry-for-help’ hypothesis provides a mechanistic explanation for previously characterized soil feedback responses to plant disease, such as the development of disease-suppressing soils upon successive cultivations of take all-infected wheat. Here, we divide the hypothesis into individual stages and evaluate the evidence for each component. We review how plant immune responses modify root exudation chemistry, as well as what impact this has on microbial activities, and the subsequent plant responses to these activities. Finally, we review the ecological relevance of the interaction, along with its translational potential for future crop protection strategies

The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity

Plants tailor their metabolism to environmental conditions, in part through the recognition of a wide array of self and non-self molecules. In particular, the perception of microbial or plant-derived molecular patterns by cell-surface-localized pattern recognition receptors (PRRs) induces pattern-triggered immunity, which includes massive transcriptional reprogramming1. An increasing number of plant PRRs and corresponding ligands are known, but whether plants tune their immune outputs to patterns of different biological origins or of different biochemical natures remains mostly unclear. Here, we performed a detailed transcriptomic analysis in an early time series focused to study rapid-signalling transcriptional outputs induced by well-characterized patterns in the model plant Arabidopsis thaliana. This revealed that the transcriptional responses to diverse patterns (independent of their origin, biochemical nature or type of PRR) are remarkably congruent. Moreover, many of the genes most rapidly and commonly upregulated by patterns are also induced by abiotic stresses, suggesting that the early transcriptional response to patterns is part of the plant general stress response (GSR). As such, plant cells' response is in the first instance mostly to danger. Notably, the genetic impairment of the GSR reduces pattern-induced antibacterial immunity, confirming the biological relevance of this initial danger response. Importantly, the definition of a small subset of 'core immunity response' genes common and specific to pattern response revealed the function of previously uncharacterized GLUTAMATE RECEPTOR-LIKE (GLR) calcium-permeable channels in immunity. This study thus illustrates general and unique properties of early immune transcriptional reprogramming and uncovers important components of plant immunity

Signals from the underground and their interplay with plant immunity

The interface between roots and their adjacent soil layer, the rhizosphere, constitutes a hotspot of microbial activity and represents one of the most diverse ecosystems on Earth. The root-associated microbial community, the microbiome, contains rhizobacteria that can change the phenotypic plasticity of their hosts and trigger a broad-spectrum form of systemic immunity, known as induced systemic resistance (ISR). Although the effect of beneficial rhizobacteria on plant growth and plant health is relatively well studied, very little is known about the early molecular processes that occur at the root-microbiome interface. In this thesis, we investigated early changes in the root transcriptome and metabolome of plant roots in response to colonization of the roots by beneficial ISR-inducing Pseudomonas rhizobacteria. We discovered that ISR-inducing rhizobacteria suppress host immune responses that are triggered by their general microbial elicitors to subsequently allow root colonization and promotion of plant growth and protection. Moreover, we uncovered the iron-mobilizing coumarin scopoletin as a major player in the chemical dialogue between plants roots and ISR-inducing members in the root microbiome. Collectively, our results show that beneficial rhizobacteria are capable of suppressing root immune responses that are activated by their general elicitors, possibly via the action of immune-suppressive effectors. This paves the way to colonize the roots and provide beneficial functions to the host plant, such as enhanced growth and protection. Within the root, the transcription factor MYB72 regulates the biosynthesis of coumarins, such as scopolin. Due to the action of the MYB72-regulated β-glucosidase BGLU42, scopolin is hydrolyzed into scopoletin, which facilitates the excretion of this metabolite into the rhizosphere. Scopoletin has a differential antimicrobial activity to which ISR-inducing rhizobacteria WCS417 and WCS358 are insensitive, but which impacts the performance of selected soil-borne pathogens. Analysis of the root-associated microbiomes of Arabidopsis roots with different scopoletin exudation patterns demonstrated a role for scopoletin in microbiome assembly. Knowledge on the molecular mechanisms that play a role in the interaction between plant roots and beneficial members of the root microbiome is essential for the development of durable biological control strategies and crops with traits that can maximize the profitable functions the root microbiome

Signals from the underground and their interplay with plant immunity

The interface between roots and their adjacent soil layer, the rhizosphere, constitutes a hotspot of microbial activity and represents one of the most diverse ecosystems on Earth. The root-associated microbial community, the microbiome, contains rhizobacteria that can change the phenotypic plasticity of their hosts and trigger a broad-spectrum form of systemic immunity, known as induced systemic resistance (ISR). Although the effect of beneficial rhizobacteria on plant growth and plant health is relatively well studied, very little is known about the early molecular processes that occur at the root-microbiome interface. In this thesis, we investigated early changes in the root transcriptome and metabolome of plant roots in response to colonization of the roots by beneficial ISR-inducing Pseudomonas rhizobacteria. We discovered that ISR-inducing rhizobacteria suppress host immune responses that are triggered by their general microbial elicitors to subsequently allow root colonization and promotion of plant growth and protection. Moreover, we uncovered the iron-mobilizing coumarin scopoletin as a major player in the chemical dialogue between plants roots and ISR-inducing members in the root microbiome. Collectively, our results show that beneficial rhizobacteria are capable of suppressing root immune responses that are activated by their general elicitors, possibly via the action of immune-suppressive effectors. This paves the way to colonize the roots and provide beneficial functions to the host plant, such as enhanced growth and protection. Within the root, the transcription factor MYB72 regulates the biosynthesis of coumarins, such as scopolin. Due to the action of the MYB72-regulated β-glucosidase BGLU42, scopolin is hydrolyzed into scopoletin, which facilitates the excretion of this metabolite into the rhizosphere. Scopoletin has a differential antimicrobial activity to which ISR-inducing rhizobacteria WCS417 and WCS358 are insensitive, but which impacts the performance of selected soil-borne pathogens. Analysis of the root-associated microbiomes of Arabidopsis roots with different scopoletin exudation patterns demonstrated a role for scopoletin in microbiome assembly. Knowledge on the molecular mechanisms that play a role in the interaction between plant roots and beneficial members of the root microbiome is essential for the development of durable biological control strategies and crops with traits that can maximize the profitable functions the root microbiome