title: 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.
authors.affiliation: Biomerit Research Centre, Department of Microbiology, National University of Ireland, University College Cork, Cork, Ireland.
authors.forename: G Louise
authors.initials: GL
authors.lastname: Mark
authors.forename: J Maxwell
authors.initials: JM
authors.lastname: Dow
authors.forename: Patrick D
authors.initials: PD
authors.lastname: Kiely
authors.forename: Hazel
authors.initials: H
authors.lastname: Higgins
authors.forename: Jill
authors.initials: J
authors.lastname: Haynes
authors.forename: Christine
authors.initials: C
authors.lastname: Baysse
authors.forename: Abdelhamid
authors.initials: A
authors.lastname: Abbas
authors.forename: Tara
authors.initials: T
authors.lastname: Foley
authors.forename: Ashley
authors.initials: A
authors.lastname: Franks
authors.forename: John
authors.initials: J
authors.lastname: Morrissey
authors.forename: Fergal
authors.initials: F
authors.lastname: O'Gara
mesh_terms: D027461:Beta vulgaris / Q000382:microbiology*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D018517:Plant Roots / Q000737:chemistry* / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity; D013559:Symbiosis