While natural and managed ecosystems like wetlands, forests, and agricultural fields often receive credit for emitting or absorbing carbon, there is an equally important yet largely overlooked contributor, acting within these ecosystems. Microbes, tiny single-celled organisms that live everywhere on Earth, are a powerhouse of carbon exchange, capable of absorbing and storing greenhouse gases like carbon dioxide and methane. Woodwell Climate researchers are studying both forests and fields to understand how natural microbial communities might be optimized into “climate heroes”, enhancing the carbon absorption capacity of natural and managed ecosystems.
One project leading the charge on this is Boreal Biosequester. Led by Associate Scientist Dr. Jennifer Watts and Senior Research Scientist Kathleen Savage along with collaborators at Arizona State University and the University of Maine Orono, this project is studying a particular class of microbe that “eats” methane, called methanotrophs.
Methane is 28 times as adept at trapping heat in the atmosphere as carbon dioxide. Today, atmospheric methane is around 2.6 times higher than during pre-industrial times. While some of these emissions are due to human sources, such as landfills and fossil fuels, around one-third of global methane emissions come from wetlands, and approximately 20-35% of wetlands are found in boreal and northern temperate forests. As a potent greenhouse gas, removal of atmospheric methane is a key natural climate solution that would help mitigate climate warming. The Boreal Biosequester team seeks to optimize the power of methane-eating microbes present in and on trees to turn methane-emitting landscapes into methane absorbers.
With funding from CarbonFix, a philanthropic organization dedicated to funding potential climate solutions, the Boreal Biosequester team has begun the first phase of the project: identifying microbial species present in the tree bark and foliage of Maine’s Howland Research Forest and studying their behavior. The researchers are investigating how trees in this northern forested wetland absorb and emit methane and how this capacity changes with environmental conditions like light, soil moisture, acidity, and temperature, to determine optimal environmental conditions for methane absorption
Much of this data is gathered from 30-meter-tall towers in the Howland Research Forest that measure methane and other gases being emitted and absorbed from this northern forest landscape. Howland boasts one of the longest global records of carbon dioxide and methane fluxes; these tower observations are paired with data collected directly from tree trunks and canopies to complete a comprehensive picture of microbial methane activity across the landscape.
“The different types of organisms that are in the trees absorbing methane have different sensitivities to temperature and how much nitrogen or sulfur or other [nutrients are] available to them,” says Watts. “What we really don’t know is: How do they live in the same space? Are there shared resources? We want to know what those preferences are.”
Boreal Biosequester team member Dr. Hinsby Cadillo-Quiroz, an ecology of microorganisms and ecosystems professor at Arizona State University, is leading the effort to isolate and study methanotrophs, sequencing their RNA and DNA to learn more about who they are and where they “like to live” in the forest.
“Plant surfaces host methanotrophs undoubtedly, although at low apparent density, so a critical question in this project is to figure out where, when, and how plant methanotrophs have the highest activity and potential to maximize their work,” says Cadillo-Quiroz. He is currently testing this question in sites around the world, including Howland.
The next phase of the Boreal Biosequester project will apply the knowledge gained from this early work to look at how the identified optimal environmental conditions can be “harnessed” to maximize methane absorption from trees using controlled greenhouse experiments.
“With greenhouse experiments, we can manipulate their environments and different tree species and then see how those microbes respond, so we can get a better sense of what those microbes like versus not, and how to optimize their behavior,” Savage says.
The final research phase of this project focuses on inoculating a forested wetland with “hardy” natural versions of these methane-eating microbes and tracing the response in landscape methane uptake. “If we can start to cultivate them successfully in the lab, we can start to select populations through natural selection,” Watts says. “We don’t want to do any direct genetic modification, but [we want to] grow the microbes that are a little bit more hardy.”
This work could yield natural climate solutions that are cost-effective and scalable for use by governments and land managers, and provide multiple benefits for carbon removal in restored or regenerating forests.
“If we understand what drives the natural activity of methanotrophs, it can inform the industry practices and plans,” Cadillo-Quiroz says.
Microbes could also be a powerful natural climate “ally” in other human-managed systems, like agricultural fields. Microbes in agricultural fields function as active climate engines by converting plant-derived carbon into stable carbon in soil, a process that could be optimized by using different land-management practices. According to Woodwell, soil microbial ecologist and biogeochemist, Dr. Taniya RoyChowdhury, properly managed croplands have the potential to become major carbon sinks.
“Global croplands have the theoretical capacity to sequester up to 2.6 gigatonnes of CO2 (carbon dioxide) annually,” RoyChowdhury says. “The research being pursued at Woodwell Climate is the critical link in the chain, providing the data needed to shift soil carbon storage from a ‘theoretical’ possibility into a ‘verifiable’ climate solution.”
RoyChowdhury is studying how regenerative agriculture practices like cover cropping could enhance a process called “necromass formation,” where carbon absorbed from the atmosphere by plants is consumed by soil microbes that then die. This carbon-rich “necromass” is then stored more permanently in the soil. This process is unique to microbes, so RoyChowdhury wants to understand how altering agricultural management practices, like cover cropping, could alter microbial activity in our favor.
“We’re trying to look at what the cover crop actually does to the microbial community. We’re genetically sequencing the microbial community in its totality and also looking at their functions,” says RoyChowdhury.
She says that working with microbes could also have co-benefits beyond carbon removal.
“Nature-based solutions [like microbes] are critical because they are the only tools we have that address the triple crisis of climate change, biodiversity loss, and food insecurity simultaneously,” says RoyChowdhury.
The other benefit of using natural climate solutions like microbes across ecosystems, RoyChowdhury says, is that once they are established, they manage themselves.
“Rightly managed natural systems are self-sustaining; once a wetland is restored or a forest is established, it continues to remove or sequester carbon and provide ecosystem services with minimal human intervention, making it a suitable strategy for long-term planetary stability,” RoyChowdhury says.
When it comes to sucking carbon dioxide out of the atmosphere, trees and forests are well-known champions. But when it comes to sequestering methane, their role is much more complicated. Forest ecosystems sometimes absorb methane, other times they emit it — creating a complex exchange of gases that scientists are only beginning to understand. Boreal forests across Canada, Alaska, Scandinavia, and Russia can sometimes be methane sinks, but they’re also set to become major emitters as climate change accelerates.
That’s the challenge the Boreal Biosequester project is tackling. By deploying newly developed methane detecting chambers at Howland Research Forest in Maine, Woodwell Climate Associate Scientist Dr. Jennifer Watts and Senior Research Scientist Kathleen Savage, along with collaborators from Arizona State University and University of Maine Orono plan to measure methane flows on a granular level to understand which bacteria consume it and how they function across the ecosystem.
Once they’ve mapped these methane-munching microbes—called methanotrophs—across varying tree species, temperatures, and seasonal shifts, the researchers want to publish their findings so governments, land trusts and foresters can enhance the activity and presence of these climate superstars, transforming ecosystems from methane sources into sinks.
Why methane matters
Methane has been overlooked in climate discussions, which largely focus on carbon dioxide, but it’s 87 times more powerful at trapping heat over a 20 year period. Atmospheric levels of methane are now 2.6 times higher than pre-industrial levels—the highest they’ve been in 800,000 years. Crucially, methane emissions from boreal forests are expected to rise or even double as temperatures rise.
Natural environments, such as wetlands and forests, account for a large portion of global methane emissions, which is why finding nature-based solutions to bring down emissions is such an important area of research. Boreal Biosequester’s approach offers the chance to turn natural sources into sinks, while also providing co-benefits such as enhanced biodiversity, wildlife habitats, flood reduction, erosion prevention, and improved air quality.
“If the methanotrophs are there, why not learn to work with them as effectively as possible?” says Watts. “If we were to work with human technology to reduce methane, you’d have to build something energy-intensive. This is a passive way to work with the forest sustainably. If we leave a forest to grow or regenerate, or if we afforest, we can both draw down CO2 and, we hope, consume methane.”
The genesis of the project
Watts and Savage were initially looking at methane sources and sinks for the US National Science Foundation. At first, they focused on soils, which were at the time considered the primary drivers of whether forests were sources or sinks. Then a groundbreaking paper revealed trees’ crucial role in methane uptake. With microbial ecologist Dr. Hinsby Cadillo-Quiroz from Arizona State University, they decided to study methane fluxes around tree trunks and canopies as well as in the soil, and sought funding from CarbonFix to carry out this study.
“When we looked at the canopy level, we could see net consumption, but soil data were all over the place,” Watts explains. “The data showed something important happening between the soils and treetops.”
The world of methanotrophs on plant surfaces is largely uncharted. The team will isolate and study these bacteria in labs while measuring methane consumption across soils, trunks, and canopies through different seasons and climates.
“We’re really the explorers venturing into this new micro-universe,” says Watts. “We know there are microbes out there, we just need to get to know them.”
Only in the last 15 years could methane gas be measured accurately at this scale. The team is uniquely positioned at Howland Forest, which has rare historical methane flux data from eddy covariance towers (structures measuring the exchange of gases) dating to 2011, plus access to both pristine and harvested forest areas for direct comparison.
The Method
CarbonFix’s grant will be used for the first phase to map methanotroph behavior and measuring fluxes across forest layers across the course of a year. Once they’ve secured additional funding, the team will identify optimal conditions for methane consumption across different tree species and environments. Next, they’ll test hypotheses in greenhouse settings, demonstrating how specific tree species can convert methane-emitting wetlands into methane-consuming ecosystems.
Finally, they’ll share findings through reports and presentations targeting governments, land trusts, foresters, and carbon markets to implement these practices in forest management.
Potential impact
For now, the team will focus on working out how methanotrophs function, and the conditions in which they thrive.
“A tiny creature, like a methanotroph, can influence a tree in many ways: it can fix nitrogen, it can clean metabolites. But the true beauty of this partnership is that a single tree could host methanotrophs in many ways and a thousand trees can host methanotrophs in a million ways. We just need to figure out how to channel this partnership to remove many tons of methane molecules. Achieving that would be a major breakthrough to help gain time against climate change,” says Cadillo-Quiroz.
The findings may extend beyond forests to landfills, agriculture, logging, or fire-damaged areas — countless applications where understanding and influencing methane fluxes through bacteria could prove transformative.
What’s more, if the team’s findings show how methanotrophs can be inoculated into new forests, they could become part of every new reforestation project.
Reforestation is urgently needed: between 2001-2023, Canada, Alaska, and the Northern US lost over 70 million hectares of forest — three times the UK’s landmass — from fire and harvest. Most of these wet soil areas are net methane emitters. Reforesting and inoculating them with methanotrophs could create carbon and methane sequestration superheroes. The team estimates targeted afforestation could remove over 10 million metric tons of methane — reducing 30-40% of high-latitude methane budgets while simultaneously sequestering CO2.
But for now, there’s lots of work to be done. The team of four are rolling up their sleeves for fieldwork and lab analysis.
“At minimum, it will be fascinating data filling knowledge gaps about methane uptake,” says Savage. “If we can remove methane short-term, we have leeway to address more challenging CO2 elements requiring extensive work.”
Watts adds: “Our group is always thinking about how what we do now will impact society later. I’m excited to develop methodologies that we can share worldwide, creating community transformation for people across the planet.”
