Microbial Communities Inside Tree Trunks: A Hidden World

While scientists have mapped microbial communities in the human gut, deep-sea ecosystems, and even clouds, the microbial societies within tree trunks have largely remained unseen until now. In a recent study published in the journal Nature, researchers analyzed around 150 trees to map the microbial communities living in 16 different species, estimating that a single mature tree hosts about a trillion bacteria in its trunk’s microbiome, with distinct communities residing in different layers.

Anaerobic Microbes and Methane Production

One of the most intriguing discoveries is the presence of anaerobic bacteria—those that do not consume oxygen—which produce methane deep within the wood. Jonathan Gewirtzman, a co-author of the study and an ecologist at Yale University, notes that what lives inside the trees is quite different from anything found elsewhere in the forest. The internal populations of the trees, he says, are more akin to those found in wetlands.

Historically, plant tissues were thought to be sterile. However, when this was debunked in the early 20th century, researchers focused heavily on roots, where many bacteria and fungi participate in soil-based nutrient cycles. What might live inside plant stems, trunks, and leaves was largely overlooked.

Research Techniques and Sample Analysis

To examine the hidden trunk biome, Gewirtzman and his colleagues drilled into living trunks to extract thin samples, which were immediately frozen using dry ice to halt microbial activity. They then separated the samples into sapwood (the outer layer) and heartwood (the inner and middle layers of the trunk), ground the frozen wood into powder, and sequenced the bacteria in each layer. To study the activity of live microbes, they also sealed the drilled holes in the trees and measured gases like methane and nitrous oxide emitted from different layers.

Evolutionary Relationships and Environmental Impact

The researchers learned that trees that are evolutionarily close tend to have similar microbiomes. The team found a profound surprise inside the trunks: in the old, inner wood, microbes were discovered that resemble those found in wetlands—anaerobic bacteria and methane producers, species suited to oxygen-free, water-saturated environments. Some bacteria in the outer layers may consume part of this methane, but the study suggests that methane and nitrous oxide-producing bacteria inside trees could create greenhouse gas emissions that scientists need to consider in their calculations.

Sharon Doty, a plant biologist at the University of Washington, says the study was fascinating because it was different from most studies: they compared inner wood versus outer wood. Doty adds that chemicals used in modern agriculture are eroding the health of plant microbiomes. By studying these natural partnerships between plants and microbes, we can understand which bacteria are important and active to reintroduce into our agricultural system.

Conclusion

The recent study unveils an unknown world of microbes inside tree trunks, highlighting the diversity of microbes living in different environments within the same organism. By using modern techniques to analyze samples, researchers were able to uncover ancient microbial communities with potential environmental impacts on greenhouse gas emissions. These discoveries may open new avenues for understanding plant-microbe relationships and present new challenges for the scientific community in how to integrate this information into their environmental and agricultural models.