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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. This study investigates how the epiphytic plant-beneficial bacterium Pseudomonas simiae WCS417 affects different root cell types of Arabidopsis thaliana using cell-type-specific transcriptomics. Bioinformatic analysis and further experimental validation demonstrate that WCS417 alters cell wall biogenesis and suberin deposition inside the root, potentially facilitating root development and bacterial colonization. Furthermore, this study reveals a role of root hairs in immune activation. [ABSTRACT FROM AUTHOR]

Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high-throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plant-associated microbiomes. Here, we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern and emerging microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture. It has been recognized for more than 100 years that soil-borne microbes play a significant role in plant growth and health. We highlight long standing and emerging concepts in plant microbe interactions in the rhizosphere in perspective of developing microbiome-assisted agriculture. [ABSTRACT FROM AUTHOR]

Bacterial flagellin is a potent host immune activator. Parys et al. (2021) and Colaianni et al. (2021) dissected effects of flagellin epitope variants on host immune detection and bacterial motility. They report in this issue of Cell Host & Microbe that Arabidopsis -associated bacterial microbiota differentially evolved flg22 variants that allow tunability between motility and defense activation. [ABSTRACT FROM AUTHOR]

Plants greatly rely on their root microbiome for uptake of nutrients and protection against stresses. Recent studies have uncovered the involvement of plant stress responses in the assembly of plant-beneficial microbiomes. To facilitate durable crop production, deciphering the driving forces that shape the microbiome is crucial. [ABSTRACT FROM AUTHOR]

The root microbiome consists of commensal, pathogenic, and plant-beneficial microbes [ 1 ]. Most members of the root microbiome possess microbe-associated molecular patterns (MAMPs) similar to those of plant pathogens [ 2 ]. Their recognition can lead to the activation of host immunity and suppression of plant growth due to growth-defense tradeoffs [ 3, 4 ]. We found that 42% of the tested root microbiota, including the plant growth-promoting rhizobacteria Pseudomonas capeferrum WCS358 [ 5, 6 ] and Pseudomonas simiae WCS417 [ 6, 7 ], are able to quench local Arabidopsis thaliana root immune responses that are triggered by flg22 [ 8 ], an immunogenic epitope of the MAMP flagellin [ 9 ], suggesting that this is an important function of the root microbiome. In a screen for WCS358 mutants that lost their capacity to suppress flg22-induced CYP71A12 pro :GUS MAMP-reporter gene expression, we identified the bacterial genes pqqF and cyoB in WCS358, which are required for the production of gluconic acid and its derivative 2-keto gluconic acid. Both WCS358 mutants are impaired in the production of these organic acids and consequently lowered their extracellular pH to a lesser extent than wild-type WCS358. Acidification of the plant growth medium similarly suppressed flg22-induced CYP71A12 pro :GUS and MYB51 pro :GUS expression, and the flg22-mediated oxidative burst, suggesting a role for rhizobacterial gluconic acid-mediated modulation of the extracellular pH in the suppression of root immunity. Rhizosphere population densities of the mutants were significantly reduced compared to wild-type. Collectively, these findings show that suppression of immune responses is an important function of the root microbiome, as it facilitates colonization by beneficial root microbiota. • 42% of the tested root microbiota are able to quench local root immune responses • Beneficial Pseudomonas can suppress root immunity by lowering environmental pH • Suppression of immunity facilitates root colonization by these beneficial microbes Many plant-root-associated microbes can trigger plant defenses. Yu et al. show that the production of gluconic acid and its derivative 2-keto gluconic acid acidifies the plant growth medium, suppressing flg22-induced root immunity to facilitate colonization by beneficial root microbiota. [ABSTRACT FROM AUTHOR]