Picture a tree. An oak, perhaps. You probably picture its bark, its canopy, its leaves catching the light. What you almost certainly don’t picture is the interior. That’s understandable, as you probably assumes it’s just a dense cylinder of static wood. But science has just turned that picture inside out.
A landmark paper published in Nature in 2025, led by researchers at Yale University, has confirmed that the wood inside living trees is not dead space. It is a thriving, ancient, and extraordinarily diverse ecosystem. A microbiome as rich and functionally vital as the one inside your own gut. And it may be one of the most consequential ecosystems on the planet.
A Microbial Census of the Forest
The research team sampled wood from the trunks, branches and roots of 150 living trees representing 16 different species across the forests of the north-eastern United States. Using cutting-edge amplicon sequencing, they conducted what they describe as the first comprehensive microbial census of living tree wood – cataloguing bacteria, archaea, and fungi that have adapted specifically to life inside a tree’s woody tissues.
The headline finding is staggering. A single tree hosts approximately one trillion bacteria in its wood. To contextualise that number, the human body contains a comparable number of bacterial cells. Trees, in other words, carry a microbial load on par with us, and they’ve likely been doing it for hundreds of millions of years, largely unnoticed.
Crucially, the researchers found that the microbial communities are starkly different in the two types of wood that make up a tree trunk. The sapwood – the outer, living layer that conducts water upward from the roots 0 hosts one community. The heartwood – the inner, structurally dead core – hosts an entirely different one. These two microbiomes share minimal overlap with each other and with any other known plant tissue or surrounding soil.
The Heartwood: a Planet Unto Itself
The heartwood microbiome, the study finds, is a particularly extraordinary ecological niche. It is dominated by specialised archaea and anaerobic bacteria. Organisms adapted to the dark, low-oxygen, chemically hostile interior of the tree. These microbes appear to be driving significant biogeochemical processes: cycling carbon, producing gases, and carrying out biochemical reactions in an environment that, for most life, would be utterly inhospitable.
This makes intuitive sense when you understand what heartwood actually is. As a tree matures, the inner wood dies and is gradually transformed, filled with defensive compounds, tannins, resins, and oils. It becomes chemically complex, structurally reinforced, and largely sealed off from the outside world. The microbes found there are specialists, adapted over geological time to that precise environment. Some are new to science entirely.
Each of the 16 tree species studied harboured a distinct microbial signature, suggesting the wood microbiome is as species-specific as the tree itself, shaped by host chemistry over millions of years of co-evolution.
The fungi present are equally remarkable. Within the heartwood, wood-decay fungi (the group that includes the organisms responsible for “heart rot,” the hollowing of ancient trees beloved by ecologists) appear alongside a rich array of endophytic fungi, organisms that live peacefully inside plant tissue without causing disease. These fungal endophytes are thought to play a role in tree defence, nutrient cycling, and potentially in the transition of living heartwood toward decomposition as a tree ages.
A New Way of Seeing
The philosophical implication of the research is as significant as its empirical findings. The authors argue that the data support viewing trees as holobionts – a term coined in evolutionary biology to describe an organism understood not as a discrete individual, but as an integrated ecological unit. A host plus all its associated microorganisms, functioning together.
We already think this way about humans. The gut microbiome is understood to be indispensable to immune function, metabolism, and even neurological health. The proposition the Yale team is making is that something analogous may be true for trees. The microbes living inside a tree’s wood may be essential partners in its physiology, health, and resilience.
This could fundamentally change how we approach forest management, conservation, and restoration. A tree is not just a tree. It is a partnership of thousands of species, evolved together over immense timescales.
If you’re genuinely curious about the science, culture, and evolving story of nature’s intelligence, The Spore Report is worth your time — a newsletter that covers the research and ideas with honesty.
Read The Spore Report →
