Novel research reveals thriving microbial life in trees
There's a thriving community of diverse microbes living in tree wood, a collaborative study from Yale Engineering and the Yale School of the Environment has found. A single tree hosts about one trillion bacteria in its woody tissue.
Trees are Earth’s largest biomass reservoir and store more than 300 gigatons of carbon. However, what is living in their wood has largely been unexplored. The study, published in Nature and led by Wyatt Arnold '24 in Yale Engineering and YSE doctoral candidate Jonathan Gewirtzman, establishes a new frontier for understanding tree physiology and forest ecology that can assist in forecasting forest response to future change and help trees adapt to climate change.
Read more • Approximately 4 minutes“Understanding these internal ecosystems gives us insights into trees' broader biogeochemical functions and how they might contribute to forest carbon cycling and nutrient exchange processes in ways we hadn't fully considered before,” Gewirtzman said.
Research on trees has focused mainly on the exposed surfaces of trees such as roots, leaves and bark. For this study, the scientists surveyed 150 living trees across 16 species in the northeast region of the U.S. They found that microbes are partitioned between heartwood (inner wood) and sapwood (outer wood) with each having their own unique microbiomes with minimal similarity to other plant tissues or ecosystem components. Inner wood is dominated by microbes that don’t need oxygen, while outer wood is dominated by microbes that do require oxygen. The microbes are actively producing gases and cycling nutrients, the study revealed.
“One of the things I found most interesting was how these microbiomes varied across different species,” said Arnold, a chemical and environmental engineer and former Ph.D. student in Jordan Peccia’s lab. “For example, sugar maples hosted a very different community than the one within pines, and these differences were consistent and conserved. I think this supports the idea that not only are these microbial communities shaped by the unique conditions within different tree species, but that these communities may have even ‘coevolved’ with trees over time.”
Co-corresponding author Jordan Peccia, noted that the approximately 3 trillion trees on Earth contribute significantly to the well-being of ecosystems and humans. Learning more about them is critical.
“We've now learned how each tree species hosts its own distinct microbial community and that this community impacts the functions and health of the tree.
Jordan Peccia
Thomas E. Golden, Jr. Professor of Chemical & Environmental Engineering
“Since the study of the human microbiome exploded more than 15 years ago, we've made important strides in human well-being and have been able to understand the beneficial impacts that microbes have on our health,” said Peccia, the Thomas E. Golden, Jr. Professor of Chemical & Environmental Engineering. “We can draw a parallel with trees. We've now learned how each tree species hosts its own distinct microbial community and that this community impacts the functions and health of the tree.”
Further research exploring wood microbiomes across different global regions and climates can lead to a better understanding of factors driving microbial diversity and function, the authors noted.
“There is a massive reservoir of unexplored biodiversity — countless microbial species living inside the world's trees that we've never documented. We need to catalog and understand these communities before climate change potentially shifts them. Some of these microbes could hold keys to promoting tree growth, conferring disease resistance, or producing useful compounds we haven't discovered yet,” Gewirtzman said.
The team of researchers included Mark Bradford, the E.H. Harriman Professor of Soils and Ecosystem Ecology; Peter Raymond, the Oastler Professor of Biogeochemistry and co-director of the Yale Center for Natural Carbon Capture; Craig Brodersen, the Howard and Maryam Newman Professor of Plant Physiological Ecology; research scientist and lecturer Marlyse Duguid; Cade Brown ’23 and Naomi Norbraten ’25.
The team spent over a year freezing, smashing, grinding and beating wood samples to develop a method that could provide the high-quality DNA required to uncover the microbiomes in the tree trunks, Bradford said.
“I was thrilled to contribute to this work given that few habitats so vast and widespread remain to be investigated, and especially one so familiar to folks as living trees,” he said. “It felt analogous to a 19th century ecologist landing on an island where the plants and animals were unfamiliar to science.”
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Published Date
Aug 6, 2025
