October 13, 2025
2 min read
Scientists Map Microbiome Hidden Deep inside Tree Trunks
Trees’ inner heartwood harbors methane-producing microbes adapted to oxygen-poor swamps and cow guts
Darrell Gulin/Getty Images
Scientists have mapped microbe populations in human guts, deep-sea ecosystems and even clouds. Yet the microbial communities inside tree trunks have remained largely unseen until now. For a recent study in Nature, researchers analyzed about 150 trees to map the communities of microbes living in 16 species. They estimate that a single mature tree hosts about one trillion bacteria in its trunk “microbiome,” with distinct communities living in different layers.
Most intriguing, the scientists found anaerobic bacteria—bacteria that don’t consume oxygen—producing methane in the deep heartwood. “It turned out what’s living inside the trees was really different from what we found anywhere else in the forest,” says the study’s co-lead author, Jonathan Gewirtzman, an ecosystem ecologist at Yale University. The trees’ interior population, he says, was more akin to that of a wetland.
For a long time plant tissues were thought to be sterile. When that was disproved in the early 1900s, researchers focused largely on roots, where many bacteria and fungi are involved in soil-based nutrient cycling. Whatever might be living within a plant’s shoots, trunks and leaves was mostly ignored.
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To examine the trunk’s hidden biome, Gewirtzman and his colleagues drilled into living tree trunks to extract thin core samples, which they immediately froze with dry ice to halt microbial activity. They then separated the cores into sapwood and heartwood (a tree trunk’s middle and innermost layers, respectively), ground the frozen wood into powder and sequenced the bacteria in each layer. To study the activity of living microbes, they also sealed holes drilled into trees and later measured gases such as methane and nitrous oxide emitted by different layers.
The researchers learned that when trees are evolutionarily close, they tend to have similar microbiomes. And the team found a surprise deep inside the trunks: “In the older and inner heartwood,” Gewirtzman says, “we saw microbes more like what you’d find in a wetland—anaerobic bacteria and methane producers,” species suited to a waterlogged and oxygen-poor environment. Some bacteria in the outer layers may consume part of that methane, the researchers found, but the study suggests that methane-producing and nitrous oxide–producing bacteria inside trees could still create greenhouse gas emissions scientists should figure into calculations.
“It is a really nice study, as they did something different from most: comparing the inner wood versus the outer wood,” says plant microbiologist Sharon Lafferty Doty of the University of Washington. Doty adds that chemicals used in modern agriculture erode the health of plant microbiomes. “By studying these natural plant-microbe partnerships, we can understand which bacteria are important and active to add back into our agricultural system,” she says.
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