24 October 2019

Plant microbes suppress costly root immune responses to boost plant growth

Blue stained arabidopsis seedlings
Blue-stained Arabidopsis seedlings growing in liquid medium (photo: Hans van Pelt

Beneficial microbes are considered a major promise for sustainable crop production. Utrecht researchers discovered that beneficial microbes on plant roots suppress host immunity to fully colonize and benefit their host plant, just like their disease-causing pathogenic counterparts. Their findings were published October 24th in Current Biology.

All plants simultaneously interact with billions of microbes, that are collectively called the plant microbiome. Some of these microbes cause disease with devastating effects on crop yields. “To prevent pathogen infection, plants have evolved a sophisticated innate immune system that recognizes conserved cell surface molecules that most pathogens possess. Activation of the plant immune system stops the invading pathogen, but this comes with fitness costs that significantly reduces plant growth”, explains last author Roeland Berendsen.

Fortunately, most microbes in the plant microbiome are harmless or even beneficial to the plant as they promote plant growth or provide protection against diseases. Interestingly, such beneficial microbes possess cell surface molecules that are very similar to those of pathogens, but do not stimulate the costly plant immune system like pathogens do.

Microscope image of Arabidopsis root
Microscope image of Arabidopsis root colonized by yellow-fluorescent plant-beneficial Pseudomonas bacteria (image: Christos Zamioudis)

Twofold benefit

“We discovered that certain beneficial root-dwelling bacteria are capable of suppressing root immunity through the excretion of specific organic acids that acidify the root environment. To our surprise we found that 42 percent of the tested root-dwelling microbiota are able to quench local root immune responses”, first author Ke Yu explains.

“This immune-modulating capacity benefits the host plant twofold: it allows the beneficial microbes to colonize the roots, and it likely prevents the growth-defense tradeoffs that are typically associated with the activation of plant immune responses”, Berendsen adds.

The Utrecht discovery discloses a novel function of the root microbiome that is essential for plant survival in nature and agriculture. This knowledge can be utilized to develop novel strategies for more sustainable microbiome-assisted agriculture.


Rhizosphere-associated Pseudomonas suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Current Biology, 24 oktober 2019. Ke Yu*, Yang Liu, Ramon Tichelaar*, Niharika Savant*, Ellen Lagendijk, Sanne J.L. van Kuijk*, Ioannis A. Stringlis*, Anja J.H. van Dijken*, Corné M.J. Pieterse*, Peter A.H.M. Bakker*, Cara H. Haney and Roeland L. Berendsen*

* Authors affiliated with Utrecht University.