Soil bacteria help plants stay calm and keep growing

Plants constantly juggle their energy between growth and defense against harmful bacteria. While the specifics of how they maintain this balance have long been unclear, researchers at Princeton University have discovered that certain soil bacteria play a crucial role in modulating plant immune responses, and allowing them to grow more efficiently.

“This is trying to get at a really big biological question where there are not good answers – about how microbiomes interface with host immune systems,” said Jonathan Conway, senior author of the study and an assistant professor of chemical and biological engineering at Princeton University. 

The research, published in the journal Cell Reports, highlights how specific microbes produce enzymes that can suppress plant immune activity, thus enabling healthier root growth.

Testing immune responses with model plants

To investigate the interaction between plants and microbes, the researchers focused on Arabidopsis, a small plant commonly used in scientific studies. They genetically engineered Arabidopsis plants to have heightened immune sensitivity to flagellin, a bacterial protein that triggers immune responses. 

This modification caused the plant’s roots to grow shorter, as its energy was diverted to immune defenses rather than root development.

The team introduced 165 bacterial species isolated from soil-grown Arabidopsis to the plants. Remarkably, 68 of these isolates, or about 41%, reduced the stunted root growth by suppressing the plant’s immune response. 

One standout species, Dyella japonica, demonstrated exceptional ability in allowing the roots to grow longer by modulating immune activity.

Unveiling the role of a key enzyme

Further investigation into D. japonica revealed a gene encoding a subtilase enzyme. This enzyme had the potential to degrade the specific part of flagellin responsible for triggering the plant’s immune response. 

Using genetic and biochemical tools, the researchers confirmed that the subtilase enzyme effectively broke down the flagellin fragment, thereby reducing the immune response and promoting root growth.

However, purifying the subtilase enzyme presented significant challenges. During a conference, postdoctoral researcher and co-first author Samuel Eastman connected with U.S. Department of Agriculture chemist Todd Naumann, who suggested purifying the enzyme using yeast cells instead of bacteria. 

Within months, Naumann successfully purified the enzyme and sent it to Princeton. “Now we can do chemistry with it, and we can actually look at this in vitro,” Eastman explained. This collaboration allowed the team to conduct more detailed studies of the enzyme’s function.

Extensive study of plants and soil bacteria 

The study was a team effort involving contributions from several researchers and students. Screening 165 bacterial isolates and verifying their immune-modulating effects required extensive work. 

“We’re able to achieve a level of investigation into this protein that wouldn’t have been possible without that collaboration,” said Eastman.

Students played a significant role in the project, including Princeton graduate Britley Jones, who contributed to screening the bacterial isolates for her senior thesis. 

Co-first author Kaeli Ficco, now a Ph.D. student at Cornell University, engineered mutant bacterial strains to confirm the genetic requirement of the subtilase gene for immune suppression. 

“I really liked how discovery-based the project was,” Ficco said, reflecting on how the work influenced her research trajectory.

Broader implications for plant immune health

Beyond studying the subtilase enzyme in D. japonica, the researchers identified similar genes in many other soil bacteria. Their assays showed that dozens of bacterial isolates could suppress flagellin-induced immunity in plants. This suggests that this mechanism may be widespread in the plant microbiome.

The team is now exploring why this enzyme may benefit both plants and bacteria. One hypothesis is that degrading pathogenic flagella reduces the ability of harmful bacteria to invade plant roots. 

“So, in that way it could be suppressing pathogens as well as the plant immune system,” said Eastman. Alternatively, the enzyme might allow certain bacteria to bypass plant defenses, potentially making plants more vulnerable to disease.

This dual possibility raises questions about applying these findings in agriculture. 

“We don’t want to compromise the immune system, but we also want plants to save that immune response for when it matters,” Eastman emphasized. 

The ultimate goal is to help plants “keep calm and keep growing.”

Future research directions

Further studies are needed to understand better how these enzymes can be leveraged in agricultural settings without increasing the plants’ susceptibility to pathogens. 

By elucidating the relationship between soil microbes and plant immunity, this research offers promising avenues for optimizing crop growth while maintaining disease resistance.

This work marks a significant step toward uncovering the intricate dynamics between plant hosts and their microbiomes, and sheds light on how these interactions can be harnessed to support sustainable agriculture.

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