One trillion microbes can live in a single tree

A single living tree can host about one trillion microbes in its wood, with distinct communities in the inner and outer layers. That is not a rounding error – it forces a rethink of what tree health and forest function really mean.

Researchers sampled 150 living trees spanning 16 species across the northeastern United States and found that these internal microbe communities are not random. They split cleanly between the inner heartwood and the outer sapwood. There is little overlap with microbes found in leaves, roots, or soil.

Jonathan Gewirtzman, a doctoral candidate at the Yale School of the Environment, led the study with support from collaborators across multiple disciplines at Yale.

Hidden worlds beneath the bark

Most research on trees has focused on what we can see, like leaves, roots, and bark. Yet forests store vast amounts of carbon across living biomass, dead wood, litter, and soils, with global stocks estimated at roughly 861 gigatons of carbon across all pools.

What happens inside wood is not a footnote for the planet. The inner trunk is not uniform. Heartwood is older, drier, and typically more sealed off, while sapwood is younger tissue that moves water and nutrients upward.

DNA reveals microbial residents

The researchers extracted high-quality DNA from woody tissues and profiled bacteria and archaea across both layers to map who lives where.

The team paired the genetic snapshots with measurements indicating microbial activity in the wood, so this was not just a catalog of dormant passengers.

Those choices matter because a microbiome is more than a roster. It is a structured community whose metabolism can change the chemistry of its home. That is exactly what the patterns in wood suggest.

Two neighborhoods in every trunk

The inner wood favored anaerobic life that does not require oxygen, a pattern seen before in studies of heartwood that reported methanogenic communities thriving in low-oxygen conditions.

The outer wood favored oxygen-using microbes suited to the sapwood’s role in water transport and air exposure. This split tracks with basic physiology and chemistry.

These communities include archaea alongside bacteria, and they do work that affects trees and ecosystems. That work includes biogeochemical processes tied to gases and nutrients that, when scaled across forests, can influence larger cycles.

Species signatures that stick

The communities were not just layered – they were species-specific. Profiles inside sugar maple differed consistently from those inside pines, and those differences held across individual trees of the same species.

This pattern is consistent with long-term host filtering and even coevolutionary pressures discussed in plant-microbe research.

“One of the things I found most interesting was how these microbiomes varied across different species,” said Wyatt Arnold, a chemical and environmental engineer and study co-lead.

“For example, sugar maples hosted a very different community than the one within pines, and these differences were consistent and conserved.”

Microbes as tree partners

Calling plants holobionts treats the organism and its associated microbes as one integrated unit. That framing is not semantics, it changes how we think about tree health, stress, disease, and even growth in the field and in cities.

These wood-dwelling partners appear to help cycle nutrients inside trunks and produce gases that may vent to the atmosphere or feed other microbes.

Scaling that up matters because forests act as a major carbon sink each year. Small changes in internal processes can add up across billions of stems worldwide.

Microbes in the carbon equation

Global assessments suggest forests hold on the order of hundreds of gigatons of carbon and continue to remove carbon dioxide from the air annually.

Knowing how much of that storage and flux depends on microbes living in wood is key for realistic models and practical management.

This is not a call to overpromise – it is a step toward tighter estimates of what forest recovery and protection can deliver.

These estimates are informed by a better handle on internal microbial metabolism. They also draw on how it changes with drought, heat, pests, and age structure across regions.

Mapping life across forests

Cataloging these communities beyond the northeastern United States will show how climate, species pools, and land use shape internal wood life.

That includes dry forests, wet tropics, plantations, and urban trees that experience pruning, compaction, and pollution in different ways.

“There is a massive reservoir of unexplored biodiversity, countless microbial species living inside the world’s trees that we’ve never documented,” said Gewirtzman. “We need to catalog and understand these communities before climate change potentially shifts them.”

Microbes matter for tree management

Internal microbiomes can influence decay resistance, wound healing, and interactions with pathogens. They may also shape a tree’s response to drought or flooding by altering internal chemistry and gas transport.

If certain microbe groups boost resistance or growth, they could lead to new diagnostics and treatments alongside breeding and silviculture.

That prospect aligns with a growing literature on shared governance between hosts and microbes in plants. This research stresses that outcomes reflect both partners.

The study is published in the journal Nature.

—–

Like what you read? Subscribe to our newsletter for engaging articles, exclusive content, and the latest updates.

Check us out on EarthSnap, a free app brought to you by Eric Ralls and Earth.com.

—–