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Nat Microbiol. 2018 Apr;3(4):470-480. doi: 10.1038/s41564-018-0129-3. Epub 2018 Mar 19.

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Author information

1
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
2
Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
3
Joint BioEnergy Institute, Biosystems Engineering Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
4
Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
5
Lincoln Science Centre, AgResearch Ltd, Christchurch, New Zealand.
6
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
7
INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Claude Bernard Lyon 1, Villeurbanne, France.
8
Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
9
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. trnorthen@lbl.gov.
10
Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. elbrodie@lbl.gov.
11
Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA. elbrodie@lbl.gov.

Abstract

Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

PMID:
29556109
DOI:
10.1038/s41564-018-0129-3

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