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| Nitrous oxide (orange and green molecules) produced at the plant root may harm certain soil bacteria, according to a new study — revealing a surprising ecological interaction that could potentially be leveraged to improve crop health. Image Credit: Christine Daniloff, MIT; iStock (CC BY-NC-ND 4.0) |
Scientific Frontline: "At a Glance" Summary: Nitrous Oxide Toxicity in Soil Bacteria
- Main Discovery: Nitrous oxide, a common greenhouse gas and byproduct of agricultural fertilizer use, actively shapes microbial communities at the plant root by exhibiting toxicity toward specific soil bacteria, contradicting the long-held assumption that the gas does not interact with rhizosphere organisms.
- Methodology: Researchers genetically removed a vitamin B12-independent enzyme from Pseudomonas aeruginosa to demonstrate its resulting sensitivity to nitrous oxide. They subsequently combined a synthetic microbial community from Arabidopsis thaliana with nitrous oxide-producing bacteria, confirming that the gas hampers the growth of neighboring soil bacteria dependent on vitamin B12 to synthesize methionine.
- Key Data: An estimated 30 percent of all bacteria with sequenced genomes are susceptible to nitrous oxide toxicity due to their strict reliance on vulnerable biological processes like vitamin B12-dependent methionine biosynthesis.
- Significance: Spikes in nitrous oxide caused by common agricultural practices, such as nitrogen fertilization and watering, can heavily disrupt intricate microbial ecosystems that are critical for nutrient access and pathogen protection in crops.
- Future Application: The timing and methods of fertilization and irrigation could be strategically managed to mitigate nitrous oxide spikes, thereby preserving beneficial microbial relationships and optimizing overall crop health.
- Branch of Science: Environmental Microbiology, Agricultural Science, and Civil and Environmental Engineering.
Plant growth is supported by millions of tiny soil microbes competing and cooperating with each other as they perform important roles at the plant root, including improving access to nutrients and protecting against pathogens. As a byproduct of their metabolism, soil microbes can also produce nitrous oxide, or \(N_2O\), a potent greenhouse gas that has mostly been studied for its impact on the climate. While some \(N_2O\) occurs naturally, its production can spike due to fertilizer application and other factors.
While it has long been believed that nitrous oxide doesn’t meaningfully interact with living organisms, a new paper by two MIT researchers shows that it may in fact shape microbial communities, making some bacterial strains more likely to grow than others.
Based on the prevalence of the biological processes disrupted by nitrous oxide, the researchers estimate about 30 percent of all bacteria with sequenced genomes are susceptible to nitrous oxide toxicity, suggesting the substance could play an important and underappreciated role in the intricate microbial ecosystems that influence plant growth.
The researchers have published their findings today in mBio, a journal of the American Society for Microbiology. If their lab findings carry over to agricultural settings, it could influence the way farmers go about everyday tasks that expose crops to spikes in nitrous oxide, such as watering and fertilization.
“This work suggests \(N_2O\) production in agricultural settings is worth paying attention to for plant health,” says senior author Darcy McRose, MIT’s Thomas D. and Virginia W. Cabot Career Development Professor, who wrote the paper with lead author and PhD student Philip Wasson. “It hasn’t been on people’s radar, but it is particularly harmful for certain microbes. This could be another knock against \(N_2O\) in addition to its climate impact. With more research, you might be able to understand how the timing of \(N_2O\) production influences these microbial relationships, and that timing could be managed to improve crop health.”
A toxic gas
Nitrous oxide was shown to be toxic decades ago when researchers realized it can deactivate vitamin B12 in the human body. Since then, it has mostly drawn attention as a long-lived greenhouse gas that can eat away at the ozone. But when it comes to agricultural settings, most people have assumed it doesn’t interact with organisms growing in the soil around the plant root, a region called the rhizosphere.
“In general, there’s an assumption that \(N_2O\) is not harmful at all despite this history of published studies showing that it can be toxic in specific contexts,” says McRose, who joined the faculty of the Department of Civil and Environmental Engineering in 2022. “People have not extended that understanding to microbial communities in the rhizosphere.”
While some studies have shown nitrous oxide sensitivity in a handful of microorganisms, less is known about how it impacts the distribution of microbial communities at the plant root. McRose and Wasson sought to fill that research gap.
They started by looking at a ubiquitous process that cells use to grow called methionine biosynthesis. Methionine biosynthesis can be carried out by enzymes that are dependent on B12 — and by other enzymes that are not. Many bacteria have both types.
Using a well-studied microbe named Pseudomonas aeruginosa, the researchers genetically removed the enzyme that isn’t dependent on B12 and found the microbe became sensitive to nitrous oxide, with its growth harmed even by nitrous oxide it produced itself.
Next the researchers looked at a synthetic microbial community from the plant Arabidopsis thaliana, finding many root-based microbes were also sensitive to nitrous oxide. Combining sensitive microbes with nitrous oxide-producing bacteria hampered their growth.
“This suggests that \(N_2O\)-producing bacteria can affect the survival of their immediate neighbors,” Wasson explains. Together, the experiments confirmed the researchers’ suspicion that the production of nitrous oxide can hamper the growth of soil bacteria dependent on vitamin B12 to make methionine.
“These results suggest nitrous oxide producers shape microbial communities,” McRose says. “In the lab the result is very clear, and the work goes beyond just looking at a single organism. The co-culture experiments aren’t the same as a study in the field, but it’s a strong demonstration.”
From the lab to the farm
In farms, soil commonly experiences spikes of nitrous oxide for days or weeks from the addition of nitrogen fertilizer, rainfall, thawing, and other events. The researchers caution that their lab experiments are only the first step toward understanding how nitrous oxide affects microbial populations in agricultural settings.
Wasson calls the paper a proof of concept and plans to study agricultural soil next.
“In agricultural environments, \(N_2O\) has been historically high,” Wasson says. “We want to see if we can detect a signature for this \(N_2O\) exposure through genome sequencing studies, where the only microbes sticking around are not sensitive to \(N_2O\). This is the obvious next step.”
McRose says the findings could lead to a new way for researchers and farmers to think about nitrous oxide.
“What’s important and exciting about this case is it predicts that microbes with one version of an enzyme are going to be sensitive to \(N_2O\) and those with a different version of the enzyme are not going to be sensitive,” McRose says. “This suggests that in the environment, exposure to \(N_2O\) is going to select for certain types of organisms based on their genomic content, which is a highly testable hypothesis.”
Reference material: What Is: Greenhouse Gas
Funding: The work was supported, in part, by the MIT Research Support Committee and a MIT Health and Life Sciences Collaborative Graduate Fellowship (HEALS).
Published in journal: mBio
Authors: Philip A. Wasson, and Darcy L. McRose
Source/Credit: Massachusetts Institute of Technology | Zach Winn
Reference Number: agri030426_01
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