Anyone who has gone for a walk in the woods can tell you that forests are impossibly dense with life. From groundhogs and squirrels scampering over rocks, to birds flitting through the canopy, to trees sprawling across the soil, every part of a forest seems to exist in a state of constant growth and motion. But life in the forest does not stop at what a hiker can see. Each plant and animal is a world unto itself, filled with tiny forms of life called microorganisms. And while these microorganisms may be invisible to the human eye, they are vital to the forest ecosystem, quietly maintaining the balance of nutrients that sustains every other living thing.
Though scientists have studied microbes on the outsides of trees, the hidden microbiomes within wood have long remained a mystery. But now, a team led by Yale researchers Wyatt Arnold (SEAS ’24) and Jonathan Gewirtzman (YSE ’26) has taken the first look at the microbes living inside tree tissue. In a new study published in Nature, they found that within the wood of trees, there exist hundreds of billions of microbes. These microbiomes are not only integral to the well-being of the trees but also affect the health of the entire forest. By peering into these tiny worlds, the team has begun unlocking a much larger story.
The Roots of Partnership
When the researchers first set out to investigate tree microbiomes, they weren’t sure what they would find. Arnold, then a PhD student in the lab of Jordan Peccia, the Thomas E. Golden, Jr. Professor of Chemical and Environmental Engineering, wanted to explore how microbial mechanics could be used to engineer solutions to environmental issues. Meanwhile, Gewirtzman, a PhD student in the laboratory of Mark Bradford, the E.H. Harriman Professor of Soils and Ecosystem Ecology, was starting to study methane emissions from trees. Learning about each other’s research interests prompted Gewirtzman and Arnold to team up to investigate trees’ methane-emitting microbes and how they vary across species and landscapes.
Although trees sequester carbon dioxide, they also emit methane, a greenhouse gas that is twenty-eight times more potent than carbon dioxide, and is rapidly increasing in the atmosphere due to its intensive emission by agriculture and fossil fuel production. Tree emissions are hypothesized to come from microbial activity. The researchers initially set out to discover the mechanism of methane production and develop a method to suppress it, especially in areas with high emissions, like wetlands. The more they looked at methane-microbial activities in trees, the more questions arose about tree microbiomes as complete units. “We kind of stumbled into this idea that people really hadn’t looked that much at tree microbiomes,” Gewirtzman said. Beginning with a mere few microbe samples, the project soon grew into a multi-year-long quest to extensively catalog and research the billions of bacteria and fungi that live inside trees.
Core Problems
To find a forest ecosystem to study, the researchers didn’t have to travel very far. Just thirty miles from Yale’s campus in New Haven lies the Yale-Myers Forest: 7,840 acres of protected woodland dedicated to the advancement of ecology knowledge. There, the team spent a warm Connecticut summer collecting samples from more than 150 trees, spanning sixteen different species native to the American Northeast.
Using a specialized tool called an increment borer, the researchers painstakingly extracted tissue from the cores of each oak, maple, and birch, taking great care not to spread pathogens or otherwise harm the trees. However, a greater challenge lay ahead: no protocol existed for extracting DNA from deep within living wood. Traditional sampling methods compromised the physical resilience and composition of the wood, which left the researchers with an incomplete census of the microbes inside. For months, Arnold and Gewirtzman tried everything they could think of to peer within the tree tissue, but nothing worked. Without a way forward, they felt they had been reduced to poking at a few soggy pieces of wood.
“There were times where we were like, ‘Are we being really stupid?’” Gewirtzman said. “For a year, I came into this building every day being like, ‘Okay, today I have like, a hammer and a pepper grinder and a bag of ice and like a sledgehammer. Let’s see if this works.’”
Indeed, one day, something worked—and it wasn’t so different from using a bag of ice and a sledgehammer. For months, the researchers had struggled to preserve the structure of the wood. But the breakthrough came when they realized that the solution was to do the opposite. Using a machine called a cryogrinder, Arnold and Gewirtzman freeze-dried the tree cores with liquid nitrogen, making them brittle while preserving the DNA. Next, the samples were ground into a fine powder called “tree dust.” From this dust, the researchers were finally able to extract the genetic material they had been searching for. Moving quickly, they processed the DNA, sent it off for sequencing, and held their breath.
Tree Cities
When the results came back, the researchers discovered that the microbial communities inside trees were just as diverse as those inside animals. Each tree species had its own unique microbiome, many of which seemed specially tuned to live in symbiosis with their arboreal hosts. For example, sugar maple trees contained a high concentration of sugar-degrading bacteria, while the communities in oaks and ashes reflected their unique variations in acidity, sap flow, antimicrobial compounds, and other biochemical conditions. “There’s compelling evidence that these taxa are involved in processes that could be important to tree health and well-being,” Arnold said.
Besides studying how microbial communities differ across species, the researchers were also interested in understanding the microbial composition in different parts of individual trees. Inside the trunk, wood is organized into two main zones. Closest to the bark is sapwood, the younger, living wood that carries water and nutrients upward from the roots. Deeper inside lies the heartwood, the older core composed mostly of dead tissue. The team found that heartwood and sapwood had very different bacterial communities: heartwood was dominated by anaerobic microbes—organisms that thrive without oxygen—whereas sapwood was rich with aerobic bacteria that require oxygen. Fungi, meanwhile, were able to colonize both zones, suggesting that they can switch between metabolic strategies or perhaps access oxygen even in low-oxygen conditions. An equally intriguing phenomenon occurs across varying vertical positions within a tree, from the roots to the branches. While the sapwood microbiome was mostly the same throughout, the heartwood microbiome varied at different heights. The researchers hypothesized that living sapwood tissue might be actively involved in regulating its microbial residents, keeping their populations stable.
But how do microbes get inside trees in the first place? The researchers tested for the presence of soil microbes as a possible source of parentage, but found that only a small percentage of the tree microbiome could have originated from the surrounding soil. It turns out that trees might inherit some of their microbes from their “parents,” much like how human mothers pass down a portion of their microbiome to their children at birth.
Seeds of Discovery
Though their findings were groundbreaking, the researchers themselves were not surprised to see that trees harbor rich, species-specific microbiomes, much like every human has a unique microbiome. What made their project novel, they said, was the way people from different academic backgrounds had come together to examine trees.
“Biologists weren’t necessarily talking to ecosystem people and thinking about greenhouse gases,” Gewirtzman said. “Those people weren’t talking to engineers and thinking about physically processing the wood. And those people weren’t necessarily talking to the biologists who understood the microbes.”
Just as this project benefited from an interdisciplinary approach, collaborations between engineering and biology may open the door for engineered solutions that address problems faced by trees. For instance, nitrogen-fixing tree seedlings are sometimes inoculated with nitrogen-fixing bacteria before planting as a way of ensuring their survival and growth. In the future, microbial inoculation strategies could be expanded to other types of microbes, positively impacting ecosystem restoration efforts.
Talking to Trees
“We viewed this paper not as the end-all-be-all for tree microbiomes, but more as a comprehensive opening to the field,” Arnold said. The results of this study could have major implications for our ability to understand, maintain, and protect vulnerable forest ecosystems.
“Just like humans, trees have a dedicated microbiome that is important for their health. The more we know about how trees and their microbes interact, the better we are equipped to manage and improve this ecosystem,” Peccia said. Many important North American tree populations have been devastated by fungal and bacterial pathogens that cause disease and death. Further surveys of tree microbiomes could help researchers understand what a healthy microbiome looks like so that they can better detect irregularities that might make trees more susceptible to attack.
Since the trees in this study were only sampled from a small area, with a relatively limited species and age range, many questions about microbial diversity remain unanswered. Would an oak tree in, say, Florida, host different microbes from one of its Connecticut cousins? Whether the microbiome in trees is influenced by geographical region, climate, age, species, or forest management is yet to be determined. Continuing with his research, Gewirtzman plans to complete a more comprehensive study that spans the East Coast of the United States to investigate such questions. This study is only the beginning of the quest to uncover the microbial diversity hidden in trees.