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

Zhalnina, Kateryna; Louie, Katherine B.; Hao, Zhao; Mansoori, Nasim; da Rocha, Ulisses Nunes; Shi, Shengjing; Cho, Heejung; Karaoz, Ulas; Loqué, Dominique; Bowen, Benjamin P.; Firestone, Mary K.; Northen, Trent R.; Brodie, Eoin L.

doi:10.1038/s41564-018-0129-3

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

Journal Article · Mon Mar 19 00:00:00 EDT 2018 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-018-0129-3· OSTI ID:1471041

Zhalnina, Kateryna ^[1]; Louie, Katherine B. ^[2];

^[3]; Mansoori, Nasim ^[4]; da Rocha, Ulisses Nunes ^[5]; Shi, Shengjing ^[6]; Cho, Heejung ^[7];

^[3]; Loqué, Dominique ^[8]; Bowen, Benjamin P. ^[2]; Firestone, Mary K. ^[9];

^[2];

^[9]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division. Earth and Environmental Sciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division. Joint BioEnergy Inst. Biosystems Engineering Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences; Helmholtz Centre for Environmental Research - UFZ, Leipzig (Germany). Dept. of Environmental Microbiology
AgResearch Ltd, Christchurch (New Zealand). Lincoln Science Centre
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division. Joint BioEnergy Inst. Biosystems Engineering Division; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; Claude Bernard Univ. Lyon 1, Villeurbanne (France). Microbiology, Adaptation and Pathogenesis
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences; Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy and Management

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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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

Sponsoring Organization:: European Union (EU); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; SC0010570; SC0016247; SC0014079; 659910

OSTI ID:: 1471041

Alternate ID(s):: OSTI ID: 1597099

Journal Information:: Nature Microbiology, Vol. 3, Issue 4; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 839 works

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