Berkeley, California, USA
January 26, 2026
Rice is a staple crop for more than half the world’s population. It’s also responsible for a significant percentage of agriculture-related greenhouse gas emissions. In a new paper published today in Nature Communications, IGI Investigators Pam Ronald at UC Davis and Jill Banfield at UC Berkeley shed new light on how rice cultivation creates greenhouse gases and suggest novel interventions that reduce methane emissions by over 50% in greenhouse trials.
The main culprit in rice paddy greenhouse gas emissions is methane, an ultra-potent gas that can trap 25x more heat than carbon dioxide. Microbes in sodden rice paddy soils make methane, but understanding the complex soil ecosystems that affect microbe metabolism has proven tricky.
In the new paper, the researchers show that increasing levels of the plant hormone PSY increases the depth of rice roots – an effect that is interesting for its potential to keep more carbon stored in the soil. Studying their modified plants, they found that deeper roots affected how microbes in the soil act. Using a powerful combination of omics techniques, the researchers were able to show that the chemicals secreted by the roots change with the levels of the hormone PSY. In turn, those chemicals from the roots affect the surrounding microbes. The team found that while specific soil microbe community members stayed the same, what the microbes were actually doing changed.
Deeper in the soil, there was a shift away from metabolic pathways that make methane and shift towards pathways that actually use up methane. The researchers saw a methane emission reduction of 58% compared to plants with typical levels of the PSY hormone and typical root architecture.
“I wasn’t expecting this outcome,” says co-first author Flor Ercoli. “We started from a plant development perspective. It was really exciting to start connecting the pieces and link what we were seeing to methane measurements.”
“The microbial community members were very similar, but their activities, what genes they were actively using, were very different. I think what the microbes are doing is trying to use the chemicals around them. They can modulate metabolic pathways depending on the chemical food resources,” says co-first author Ling-Dong Shi, a postdoctoral researcher in the Banfield lab.
Flor Ercoli
Lingdong Shi
After seeing the powerful effects of the roots on the surrounding microbes, the researchers wondered if it would be possible to get the same effect without genome engineering.
They tried taking the chemicals secreted by the rice roots and applying them directly to the soil of other rice strains and saw similar reductions in methane emissions.
“We wanted to recapitulate the methane reduction using the chemistry from the roots. We collect the take-aways, put it on the soil, and see the same effect,” says Ercoli.
The team also examined the effect of the changes on rice yield, a key factor for implementing any changes in how rice is grown.
“While the initial rice variety we tested had lower yield with the deeper roots and reduced methane, we tried making the same genetic change using a different member of the same plant hormone family and saw no decrease in yield. So, we know it’s possible to reduce methane without reducing yield. This opens an opportunity to rethink the type of chemistry that could be added to the soil.,” says Ercoli. In other words,recreating the effect by using soil additives of genetically modifying the elite cultivars that farmers like to grow.
The big take away: two new ways to reduce methane emissions from rice, using either genome engineering to change root architecture, or simply applying specific compounds to soil of the typical rice plants.
“Basically, rice plants affect the microbes through secreting compounds,” says Shi. “The chemical compounds are the real factors that control methane dynamics. This strategy can be achieved by editing rice genomes, but also by modifying how we grow rice, for example, by changing nutrients in the soil. It’s a pretty generalizable strategy.”
Funding for this research was provided by the Chan Zuckerberg Initiative and the Bill and Melinda Gates Foundation. This research is based on foundational research supported by federal funds from the Joint BioEnergy Institute and U.S. Department of Energy.
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