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

journal contribution
posted on 2023-05-03, 16:00 authored by Kateryna Zhalnina, Katherine Louie, Zhao Hao, Ulisses Nunes da Rocha, Shengjing ShiShengjing Shi, Heejung Cho, Ulas Karaoz, Dominique Loqué, Benjamin Bowen, Mary Firestone, Trent Northen, Eoin Brodie
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.


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© 2019 Springer Nature Publishing AG


  • English

Does this contain Māori information or data?

  • No


Springer Nature

Journal title

Nature Microbiology




Zhalnina, K., Louie, K. B., Hao, Z., Nunes da Rocha, U., Shi, S., Cho, H., … Brodie, E. L. (2018). Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature Microbiology, 3, 470–480. doi:10.1038/s41564-018-0129-3

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