The effect of root exudates on the transcriptome of rhizospherePseudomonasspp

Abstract

Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular-weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialogue between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.

The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of Burkholderia pyrrocinia strain P10

“…The expression levels of genes encoding proteins in the ribose transport system (RbsC and RbsA), the L-arabinose transport system (AraFHG), and the D-xylose transport system (XylH and XylG) were also up-regulated. A previous study detected similar up-regulated expression levels for genes related to carbohydrate metabolism and transport in Pseudomonas uorescens treated with the Brachypodium distachyon RE; these changes may contribute to the differential a nity of Pseudomonas for host plants and/or determine which strains can ourish in response to root growth and changes in environmental conditions [10]. Similar ndings were reported for Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424, and Rhizobium mesoamericanum STM3625 treated with the Mimosa pudica RE [28].…”

“…In contrast, a 20-to 22-h exposure to Brachypodium REs has inhibitory effects on sulfur transport and metabolism in Pseudomonas species, possibly because the cysteine and cystine in the REs repress the Pseudomonas sp. pathways controlling the catabolism of sulfonates and taurine [10]. However, Pimenta et al observed that the expression levels of genes involved in sulfur metabolism (e.g., genes related to sulfur transport, sulfate activation and reduction, and sulfonate transport) are up-regulated by REs.…”

“…Some RE components may function as signaling molecules that regulate the rhizosphere microbial activity [7,8,9]. In addition, up to 40% of photosynthetically xed carbon is released by plant roots in the form of exudates and secretions, lysates, and mucilages and then serve as a carbon and energy source for rhizosphere microorganisms [10]. Accordingly, REs also in uence the colonization and growth-promoting effects of PGPR added to the soil.…”

The Multiple Promoting Effects of Suaeda glauca Root Exudates on the Growth of Alfalfa under NaCl Stress

“…This is because REs contain a large number of compounds that act as signals for establishing and regulating plants' interactions with microorganisms. The composition and activity of soil microorganisms further affect soil enzyme activity and plant functional characteristics [76][77][78]. Therefore, it has been suggested that REs provide additional carbon and energy to the microorganisms in saline soil, stimulate the growth and metabolic activities of microorganisms, and then increase the activities of urease and neutral phosphatase, which are helpful for plants to absorb nitrogen and phosphorus more effectively [76,78].…”

Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associatedPseudomonas stutzeriA1501

“…These carbon sources may be important for the bacterial growth of rice roots in certain ecological niches. For instance, glucose, some branched-chain amino acids, formate, and betaine support the growth of Pseudomonas in the rice root rhizosphere or improve the resistance of rice (38). Overall, Hfq directly regulates the expression of (> 200) genes that encode transporters of carbon sources and other nutrients and whose expression was significantly altered.…”