Dynamic Root Exudate Chemistry and Microbial Substrate Preferences Drive Patterns in Rhizosphere Microbial Community Assembly

Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments.

The Science

Show impact of plant exudates on soil microbiome.

  • Large-scale microbial isolation used to create a collection of relevant rhizosphere isolates.
  • Microbial community analysis and comparative genomics used to define dynamics of microbial isolates in rhizosphere and identify microbial traits selected in the rhizosphere.
  • Exometabolomics used to determine plant exudate composition and substrate uptake preferences of rhizosphere microorganisms.

The Impact

  • Changes in the root exudate chemistry during plant development and preferential consumption of specific exudate compounds by soil microorganisms is a key mechanism by which plants shape their rhizosphere microbiome.
  • Provides a mechanistic underpinning of rhizosphere microbial community assembly and an attractive direction for the beneficial manipulation of the rhizosphere microbiome.

Summary

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. In this paper, using a combination of comparative genomics and exometabolomics, researchers 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, researchers 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.

References

Zhalnina, K., K. B. Louie, Z. Hao, N. Mansoori, U. N. da Rocha, S. Shi, H. Cho, U. Karaoz, D. Loqué, B. P. Bowen, M. K. Firestone, T. R. Northen, E. L Brodie. 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.