Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls

Persistent organic pollutants, such as polychlorinated biphenyls (PCBs), are a global problem. We demonstrate enhanced depletion of PCBs using root-associated microbes, which can use plant secondary metabolites, such as phenylpropanoids. Using a "rhizosphere metabolomics" approach, we show that phenylpropanoids constitute 84% of the secondary metabolites exuded from Arabidopsis roots. Phenylpropanoid-utilizing microbes are more competitive and are able to grow at least 100-fold better than their auxotrophic mutants on roots of plants that are able to synthesize or overproduce phenylpropanoids, such as flavonoids. Better colonization of the phenylpropanoid-utilizing strain in a gnotobiotic system on the roots of flavonoid-producing plants leads to almost 90% removal of PCBs in a 28-d period. Our work complements previous approaches to engineer soil microbial populations based on opines produced by transgenic plants and used by microbes carrying opine metabolism genes. The current approach based on plant natural products can be applied to contaminated soils with pre-existing vegetation. This strategy is also likely to be applicable to improving the competitive abilities of biocontrol and biofertilization strains.