Soil bacteria help plants balance growth and immunity

Plants face the constant challenge of allocating energy between growth and defense. While growth ensures survival and reproduction, defense protects against harmful bacteria.

Until now, scientists struggled to explain how plants achieve this balance. Researchers at Princeton University recently uncovered new insights into this process, revealing the surprising role of soil bacteria in managing plants’ immune responses.

How soil bacteria help plants

Published in the journal Cell Reports, the study explores how certain soil bacteria impact plant immunity. The bacteria produce enzymes that reduce immune activity in plants, enabling their roots to grow longer.

This discovery sheds light on how plants interact with microbiomes without triggering constant immune responses.

“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, the study’s senior author and an assistant professor of chemical and biological engineering.

“It’s a small step in the direction of trying to understand how microbes live on hosts – either plants or humans or other animals – all the time and don’t activate our immune responses constantly.”

Balancing health and growth

The team focused on Arabidopsis, a small mustard plant often used in research. They engineered Arabidopsis seedlings with heightened sensitivity to flagellin, a bacterial protein that typically activates immune responses.

On exposure to flagellin, these plants directed energy toward immunity, resulting in stunted root growth.

To identify bacteria that could suppress this immune response, the researchers introduced 165 bacterial species to the seedlings.

Remarkably, 41% of these isolates suppressed the stunted growth response, allowing roots to grow longer. Among these, Dyella japonica emerged as particularly effective.

Enzyme regulates immune system response

The researchers discovered that D. japonica, a soil bacterium, produces an enzyme called subtilase. This enzyme breaks down flagellin, a protein that normally triggers a plant’s immune response.

By degrading flagellin, subtilase prevents the plant’s immune system from activating unnecessarily, enabling the roots to grow without being stunted.

To confirm subtilase’s role, the team used genetic and biochemical techniques. These methods demonstrated that subtilase directly modulates the plant’s immune response, proving its critical function.

Purifying the subtilase enzyme posed significant challenges, as obtaining a pure protein is essential for detailed analysis. A breakthrough came when Todd Naumann, a USDA chemist, suggested purifying the enzyme using yeast cells instead of bacteria.

This alternative approach worked effectively, allowing the researchers to proceed with advanced studies on the enzyme’s properties and functions.

“Now we can do chemistry with it, and we can actually look at this in vitro,” said co-first author Samuel Eastman.

Dual role of soil bacteria

The findings suggest that many soil bacteria may use similar enzymes to influence plant growth and immunity. This raises intriguing questions about the potential benefits for both plants and bacteria.

One theory is that the enzymes prevent pathogens from invading plant roots by disabling their flagella. Alternatively, the enzymes might help pathogens evade detection, potentially increasing the risk of disease.

“So, in that way it could be suppressing pathogens as well as the plant immune system,” Eastman noted. However, he warned of the risks in agricultural applications.

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

Improving crop growth and plant health

The team’s work opens doors to harnessing beneficial bacteria for agriculture while minimizing risks. With further research, these findings could lead to innovative ways to improve crop growth without compromising plant health.

For now, scientists are one step closer to understanding the delicate balance of growth and defense in plants.

The study was a team effort involving nine Princeton researchers, including six undergraduates. Senior thesis projects played a vital role, such as that of Britley Jones from the Class of 2023.

Kaeli Ficco, another key contributor and a Princeton graduate, engineered mutant bacterial strains to confirm the genetic basis of immune suppression.

“I really liked how discovery-based the project was,” Ficco said, reflecting on her contributions.

The study is published in the journal Cell Reports.

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