Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions

Abstract

Molecules exuded by plant roots are thought to act as signals to influence the ability of microbial strains to colonize the roots and to survive in the rhizosphere. Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the Pseudomonas aeruginosa PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of P. aeruginosa in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis.Pseudomonas ͉ Rhizosphere colonization

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

“…Several studies have addressed the transcriptomics of the rhizosphere (Diehn and Relman, 2001;Mark et al, 2005;Matilla et al, 2007;Ramachandran et al, 2011), but always using a controlled approach with a single bacterium, one or a few plants in sterile substrates or purified root exudates. In this study, we used a metatranscriptomic approach and assessed the whole microbial community associated with willow roots growing in non-sterile soil from a contaminated site.…”

“…In the rhizosphere of various plants growing in non-contaminated soils, the shikimate and protocatechuate transport systems of Rhizobium leguminosarum were induced, and, when these genes were mutated, it led to reduced efficiency in rhizosphere colonization (Ramachandran et al, 2011). When exposing Pseudomonas aeruginosa to root exudates, genes related to aromatic compound catabolism and protocatechuate 3,4-dioxygenase were significantly upregulated (Mark et al, 2005).…”

Effects of Azospirillum brasilense on growth and yield compounds of maize grown at nitrogen limiting conditions

“…In this case, based on the understanding of Hallmann et al (1997) and Saubidet et al (2002) it is guessed that under the employed N fertilizer level, plants were not able to provide A. brasilense with an adequate carbon compounds supply to sustain maximal cultivar's growth and yield. As discussed in Araújo et al (2015), under limited N availability plants cannot produce sufficient root exudates, which act as signal to influence the ability of strains to colonize soil by horizontal movement or to survive in the rhizosphere (Mark et al, 2005;Bashan and Levanony, 1987).…”

Plant responses to plant growth-promoting rhizobacteria

“…Numbers of resistance-inducing bacteria may be changed, or their expression of resistance-inducing traits may be altered (Mark et al 2005). Plants commonly react to root colonization by rhizobacteria by increasing the release of exudates, and quantity and composition of root exudates vary with plant developmental stage (Phillips et al 2004).…”