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Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12558-12565. doi: 10.1073/pnas.1820691116. Epub 2019 May 31.

Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome.

Author information

1
Department of Chemical Engineering, Stanford University, Stanford, CA 94305.
2
Department of Bioengineering, Stanford University, Stanford, CA 94305.
3
Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
4
Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
5
Department of Chemical Engineering, Stanford University, Stanford, CA 94305; sattely@stanford.edu.
6
Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305.

Abstract

The factors that contribute to the composition of the root microbiome and, in turn, affect plant fitness are not well understood. Recent work has highlighted a major contribution of the soil inoculum in determining the composition of the root microbiome. However, plants are known to conditionally exude a diverse array of unique secondary metabolites, that vary among species and environmental conditions and can interact with the surrounding biota. Here, we explore the role of specialized metabolites in dictating which bacteria reside in the rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated bacteria to detect community shifts that occur in the absence of the secreted small-molecule phytoalexins, flavonoids, and coumarins. We find that lack of coumarin biosynthesis in f6'h1 mutant plant lines causes a shift in the root microbial community specifically under iron deficiency. We demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. thaliana root bacterial community by inhibiting the proliferation of a relatively abundant Pseudomonas species via a redox-mediated mechanism. This work establishes a systematic approach enabling elucidation of specific mechanisms by which plant-derived molecules mediate microbial community composition. Our findings expand on the function of conditionally exuded specialized metabolites and suggest avenues to effectively engineer the rhizosphere with the aim of improving crop growth in iron-limited alkaline soils, which make up a third of the world's arable soils.

KEYWORDS:

coumarins; plant microbiome; plant specialized metabolism; synthetic communities

PMID:
31152139
PMCID:
PMC6589675
[Available on 2019-11-30]
DOI:
10.1073/pnas.1820691116

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