Plant roots are constantly interacting with various species of microbes which have varying degrees of impact on plant growth. The rhizosphere, known as the zone immediately surrounding plant roots is mostly home to harmless microbes, but some are pathogenic and detrimental to plant health. There are also good bacteria living in the rhizosphere which are able to do things like stimulate root growth, control abiotic stress and disease, and even help clean up contaminated soil.^1,2 Understanding the microbes living in the rhizosphere, especially the bacteria, or ‘rhizobacteria,’ has become an important field of study in the effort to improve agricultural practices. In addition to mitigating the effects of pathogenic bacteria, understanding and harnessing the effects of beneficial bacteria will be important for developing sustainable crop production methods and practices. Published in Current Biology in October 2019, Yu et al. uncover a mechanism used by beneficial bacteria to effectively colonize host plants and promote their growth by suppressing plant immune responses.³

Since plant roots are always interacting with rhizobacteria and other microbes in the rhizosphere, plants have evolved an innate immune system to defend themselves against microbes which can cause them harm.^4-6 The innate immune system detects microbe invasion through pathogen/microbe-associated molecular patterns (PAMPs/MAMPs): physical attributes of a microbe which are recognized by receptors on host plant cells.^5-7 Flagellin, the material which makes up bacterial flagella (the ‘tail’ like appendages used for movement) is a well-known MAMP, and is recognized by a receptor-like kinase on the plant cell surface called FLS2.⁵  Perception of flagellin by FLS2 results in a series of downstream signalling cascades, activating genes involved in the plant’s defense response and inhibiting plant growth.⁵

Since many microbes possess the same physical attributes like flagellin, plant defense mechanisms are not necessarily able to differentiate between pathogenic and beneficial or harmless microbes, which can lead to a phenomenon known as the ‘growth-defense trade-off’.⁴  Both growth and initiating defense mechanisms require large energy expenditures, so the plant must prioritize which action is most essential for its survival.⁴ In nearly every case, defense takes precedence over growth, which is seemingly problematic when the environment in which plants grow is full of microbes recognized by plant immune systems. However, it has been shown that many microbes are actually able to promote growth and protect plants against pathogenic microbes by competing for nutrients or producing antibiotics.^1,2,4 What’s more, many beneficial microbes have evolved methods to actively evade plant immune systems so they do not initiate a defense response and can help the plant conserve energy to use for growth.^2,4,8,9

A story of beneficial microbes which can evade host plant immune systems comes from Yu et al. who show that a family of rhizobacteria called Pseudomonas are able to avoid plant detection by producing an acid which lowers the rhizosphere pH. The Pseudomonas family has strains which can be both pathogenic and beneficial to plants, but still retain very similar physical characteristics, meaning they should be perceived the same way by the plant’s immune system.^8-11 The Yu et al. study looked at two beneficial Pseudomonas species in particular, Pseudomonas capeferrum WCS358 and Pseudomonas simiae WCS417, both of which were able to limit plant immune responses triggered by flagellin. Furthermore, 42% of all other microbes present in the soil samples where the Pseudomonas species were found were also able to quench plant immune responses, allowing the microbes to successfully colonize the host plant’s roots. However, before concluding these Pseudomonas species were indeed suppressing host immune responses instead of simply avoiding them, the team confirmed the rhizobacteria had not evolved novel flagellin which couldn’t be perceived by FLS2. This finding points to the importance of suppressing host plant immune systems for the general function of the root microbiome.

To better understand the mechanism by which these Pseudomonas species were able to suppress host immune systems, the team embarked on a functional study looking at MAMP-reporter gene activation in Arabidopsis roots under different physiological conditions. The team created three Arabidopsis transgenic lines with the β-glucoronidase (GUS) reporter gene fused to genes which are known to be activated in response to flagellin. Normally, in the presence of flagellin, one of these transgenic Arabidopsis roots would turn blue, indicating the activation of a defense response. However, when the transgenic roots were treated with the two Pseudomonas species, there was no defense gene activation, indicating something in the bacteria was suppressing immune system activation. In order to determine what exactly the bacteria was doing to evade flagellin perception, the team treated the roots with just the solution in which the bacteria lived, both heat treated and not, but without the bacteria themselves. This experiment yielded the same results as live bacteria treatment, indicating the bacteria were secreting some type of compound that was not a protein which enabled them to avoid detection.

In an effort to uncover genes which may be regulating the bacteria’s evasion of flagellin detection, the team created a series of Pseudomonas mutants by randomly inserting mini-Tn5 transposons into their genomes. The mutants were assessed for their failure to suppress flagellin-induced plant immune responses, visualized with GUS expression. Two mutants fitting the criteria were identified and analyzed to find the transposons were inserted into the PqqF and CyoB genes, respectively. PqqF and CyoB code for a protease and an oxidase both involved in bacterial oxidative fermentation of glucose which results in the production of gluconic acid and its derivative 2-keto-D-gluconic acid. The team confirmed the roles of PqqF and CyoB in gluconic acid production and found that abolishing one or both of the genes’ functions resulted in significantly higher pH of the root environment compared to bacteria with functioning copies of the two genes. Since the group had only looked at PqqF and CyoB in two specific Pseudomonas species, they decided to see if the genes were conserved across the Pseudomonas family, which they found to be true. Taken together, the results from the Yu et al. study indicate that beneficial Pseudomonas species acidify their environment by producing gluconic acid in order to suppress host immune responses.

The discovery that beneficial Pseudomonas rhizobacteria can actively suppress host immune systems by secreting gluconic acid into the root environment sheds light on how some bacteria are able to mitigate growth-defense trade-offs suffered by host plants. By developing a method to boost their own growth, Pseudomonas rhizobacteria have also improved the growth of their host, a mechanism which could be harnessed to develop methods aimed at improving plant growth in an agricultural setting.