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 dialog 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.
Highlights
Plants are meta-organisms or holobionts that rely in part on their microbiome for specific functions and traits
By profiling transcriptomes of these strains during growth in root exudates of B. distachyon, we revealed the diversity of cellular pathways and physiological responses that underlie the establishment of mutualistic interactions between beneficial rhizobacteria and the host plant
Metabolomics analysis of lyophilized root exudates revealed the presence of numerous plant metabolites, 86 of which were identified by matching their spectra to the LECO/Fiehn Metabolomics library (Supplementary Table 3)
Summary
Plants are meta-organisms or holobionts that rely in part on their microbiome for specific functions and traits. Primary root exudates include simple and complex sugars, amino acids, polypeptides and proteins, organic, aliphatic and fatty acids, sterols, and phenolics (Nguyen, 2003; Badri and Vivanco, 2009; Badri et al, 2009) These compounds serve as carbon and energy sources for rhizobacteria, and the presence of the intact corresponding catabolic pathways is essential for competitive colonization of roots and disease suppression (Lugtenberg et al, 2001; Kamilova et al, 2005; Lugtenberg and Kamilova, 2009). We confirmed the capacity of B. distachyon Bd21 to serve as a host for rhizobacteria of the P. fluorescens group in preliminary greenhouse assays with biocontrol strains P. synxantha 2-79, P. brassicacearum Q8r1-96, and P. protegens Pf-5 Results of these experiments revealed that all strains successfully established and colonized the roots of Brachypodium (Supplementary Table 1). The diversity of microbial genes perturbed by root exudates reflects the importance of the variable genome in adaptation of individual strains of Pseudomonas to the rhizosphere lifestyle
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
