Scientists map microbiome hidden deep in tree trunks

Scientists map microbiome hidden deep in tree trunks

By Saugat Bolakhe edited by Sarah Lewin Frasier

Scientists have mapped populations of microbes in human intestines, deep-sea ecosystems, and even clouds. However, microbial communities within tree trunks have remained virtually invisible until now. For a recent study in NatureThe researchers analyzed about 150 trees to map the communities of microbes living in 16 species. They estimate that a single mature tree harbors around a trillion bacteria in the “microbiome” of its trunk, with distinct communities living in different layers.

Most intriguingly, the scientists found anaerobic bacteria (bacteria that do not consume oxygen) that produce methane deep in the heartwood. “It turned out that what lives 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 interior population of trees, he says, was more similar to that of a wetland.

For a long time it was thought that plant tissues were sterile. When this was disproven in the early 20th century, researchers focused primarily on roots, where many bacteria and fungi participate in soil nutrient cycling. Anything that might be living inside the shoots, trunks and leaves of a plant was largely ignored.

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To examine the hidden trunk biome, Gewirtzman and his colleagues drilled holes into live tree trunks to extract thin samples of the core, which they immediately froze with dry ice to stop microbial activity. They then separated the cores into sapwood and heartwood (the middle and inner layers of a tree trunk, 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 in trees and then measured gases such as methane and nitrous oxide emitted by different layers.

The researchers found that when trees are evolutionarily close, they tend to have similar microbiomes. And the team found a surprise deep in the trunks: “In the oldest, inner heartwood,” Gewirtzman says, “we saw microbes more like those you would find in a wetland: anaerobic, methane-producing bacteria,” species suited to a waterlogged, oxygen-poor environment. Some bacteria in the outer layers can consume some of that methane, the researchers found, but the study suggests that methane- and nitrous oxide-producing bacteria inside the trees could still generate greenhouse gas emissions that scientists should include in calculations.

“It’s a really interesting study because they did something different than most: compare interior wood to exterior 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 associations between plants and microbes, we can understand which bacteria are important and active to add back to our agricultural system,” he says.

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