Between a third and half of all soil carbon on Earth is stored in peatlands, says Tom and Marie Patton Distinguished Professor Joel Kostka. These wetlands — formed from layers and layers of decaying plant matter — span from the Arctic to the tropics, supporting biodiversity and regulating global climate.

“Peatlands are essential carbon stores, but as temperatures warm, this carbon is in danger of being released as carbon dioxide and methane,” says Kostka, who is also the associate chair for Research in the School of Biological Sciences and the director of Georgia Tech for Georgia’s Tomorrow. Understanding the ratio of carbon dioxide to methane is critical, he adds, because while both are greenhouse gasses, methane is significantly more potent.

Kostka is the corresponding author of a new study unearthing how and why peatlands are producing carbon dioxide and methane. 

The research, “Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter,” was published this summer in Nature Communications, and was led by co-first authors Borja Aldeguer-Riquelme, a postdoctoral research associate in the Environmental Microbial Genomics Laboratory, and Katherine Duchesneau, a Ph.D. student in the School of Biological Sciences.

The study builds on a decade of research at the Oak Ridge National Lab’s Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, a long-term research project in Minnesota that allows researchers to warm whole sections of wetland from tree top to bog bottom.

“Over the past 10 years, we’ve shown that warming in this large-scale climate experiment increases greenhouse gas production,” Kostka says. “But while warming makes the bog produce more methane, we still observe a lot more CO2 production than methane. In this paper, we take a critical step towards discovering why — and describing the mechanisms that determine which gases are released and in what amounts.”

Methane mystery

The subdued methane production in peatlands has been a long-standing mystery. In water-saturated wetlands, oxygen is scarce, but microbes still need to respire — a type of ‘breathing’ that allows them to produce energy for metabolic function. Without oxygen, microbes use nitrate, sulfate, or metals to respire — still releasing carbon dioxide in the process. However, if these ingredients aren’t present, microbes ‘breathe’ in a way that releases methane.

Since nitrate, sulfate, and metals are relatively rare in peatlands, methane production should be the most likely pathway, but surprisingly, observations show the opposite. “In both fieldwork and lab experiments, peatlands produce much more carbon dioxide than methane,” Kostka explains. “It’s puzzling because the soil conditions should help methane production dominate.”

To solve this mystery, the team leveraged a suite of cutting-edge genetic tools called “omics” —  metagenomics (studying DNA), metatranscriptomics (studying RNA), and metabolomics (a technique used to study the “leftovers” of metabolism), providing a detailed look under the hood of the microbial “engine” that cycles organic matter in wetlands. It also gave a new window into the diversity of soil microbes in wetlands: 80 percent of the organisms identified in the study were new at the genus level.

‘Omics’ innovations

Over the course of several years, the team collected samples from a peatland enclosed in an experimental chamber that was slowly warmed, then analyzed the samples using omics to see how they changed. Initially, they hypothesized that warming the soil would cause microbial communities to change quickly. “Microbes can evolve and grow rapidly,” Kostka says. “But that didn’t happen.”

The DNA-based methods showed that while the microbial communities stayed largely stable, the bog did release more greenhouse gasses as it warmed. To assess the metabolic potential of the microbes, Duchesneau and Aldeguer-Riquelme constructed microbial genomes, investigating how they were decomposing the organic matter in peatlands and cycling carbon.

“We found that microbial activity increases with warming, but the growth response of microbial communities lags behind these changes in physiological or metabolic activity,” Kostka says. He cautions that this doesn’t necessarily mean that wetland communities won’t change as climates warm — just that these shifts might come behind metabolic ones. 

A diversity of discoveries

And the methane? The team believes that microbes may be breaking down organic matter to access the key ingredients for producing carbon dioxide — nitrate, sulfate, and metals — though more research is currently underway to investigate this.

“Doing this type of integrated omics research in soil systems is still incredibly difficult,” Kostka says. The challenge is multifaceted: the research leverages years of experiments, long-term datasets, advanced laboratory techniques, and fieldwork innovations. 

At SPRUCE, experimental chambers are about 1,000 square feet. While it’s an impressive experimental setup, researchers still must be careful: “We need to take soil samples for many years, so if we take too many, there’d be no soil left!” Kostka explains. “Part of our research involves developing better, non-destructive sampling techniques.”

The other challenge lies in what makes these peatlands so unique: it’s very hard to detect small changes because of the sheer diversity of organisms present. “Every time we conduct this type of research, we learn more about these incredible systems,” he says. “There’s always something new.”

DOI: https://doi.org/10.1038/s41467-025-61664-7

Funding: The Office of Biological and Environmental Research, Terrestrial Ecosystem Science Program and Genomic Science programs, under the US Department of Energy (DOE); the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program. The SPRUCE experiment is funded by the Biological and Environmental Research program in the U.S. Department of Energy’s Office of Science.