One Tree, One Trillion Microbes: Understanding the Tree Microbiome

Overview of the bacterial and archaeal microbiome of black oak (Quercus velutina). Each donut plot shows the relative composition of taxonomic classes present from a different tree sample type. More specifically, sample types consist of: a) bark, b) sapwood, c) heartwood, d) fine roots, e) coarse roots, f) mineral soil, g) organic soil, h) leaf litter, i) heart-rot, j) branches, and k) leaves. Source: Wyatt et al. (2024) Figure 4a.

When we think of forests, we tend to picture towering trees and dense vegetation, populated by birds, mammals, and insects. Within this familiar scene, however, lies an invisible microbial world teeming with life. In fact, new research by Wyatt and colleagues, led from Yale University and published in August 2024 in the journal Nature, shows that a single tree trunk alone can harbor more than a million microbes in its woody tissue. That’s about one bacterial cell for every 20 plant cells!

Trees are foundational to terrestrial ecosystems, forming the backbone of forest habitats, supporting the myriad species that depend on them, and providing essential ecosystem services. They store over 300 gigatons of carbon globally and support a vast range of economic activities, including the production of food, fuel, and fiber, with an estimated global value of $9 trillion. Despite their ecological and economic importance, surprisingly little is known about the tree microbiome, which is the collective genetic material of microbes living inside trees, and in particular about the microbial communities associated with wood, which is the largest reservoir of biomass on Earth. This knowledge gap is significant, because in other species (both plants and animals) microbial communities have profound effects on host health. In humans, for example, the gut microbiome aids digestion, strengthens the immune system, influences susceptibility to diseases such as cardiovascular conditions and certain cancers, and even affects mood and mental health. Plants benefit in similar ways, with microbial partners boosting growth, enhancing drought tolerance, and protecting against disease, amongst other functions.

In the new study, Wyatt and colleagues surveyed the wood-associated microbiome of over 150 living trees across 16 species in the northeastern United States, representing 11 genera with a global distribution across 151 countries. This included trees commonly found in the Montreal area, such as maples and oaks. The researchers collected wood samples from the trunks of 158 trees, as well as soil samples from around each tree. After extracting DNA from these samples, they sent the material to a lab for sequencing of key marker genes (16S and ITS) which allowed them to identify different types of microorganisms. The team then analyzed the sequencing data, comparing the recovered gene sequences to large databases to determine which microbial species were present and how communities differed between tree tissues and their surrounding environment.

One of the first things that researchers observed is that microbes inside wood form a specialized, self-contained community rather than being a random mix washed in from the soil or other parts of the tree. In fact, for some tree species examined, only about 3% of the microbes found in the wood were also present in the soil around the tree. Even across samples from bark, branch wood, leaves, coarse and fine roots, and even heart rot, the researchers found very little overlap in the types of microbes present, indicating that the wood microbiome is distinct from other tree-associated microbial communities. This is significant because it suggests that each part of the tree harbors a distinct microbiome with unique functional traits, capable of interacting with the tree host and its environment in different ways.

Given that the microbial communities differed so clearly between tree parts like leaves and wood, the researchers next examined how fine-scaled these differences could be. They compared communities in two types of wood: heartwood, which is the dense, older, non-living central core of the tree, and sapwood, which is the outer, living layer responsible for transporting water and nutrients. Again, they found that these niches harbour different microbial communities, highlighting the remarkable degree of specialization. The authors suggest that these differences are driven by the contrasting conditions within the woody tissues: heartwood is broadly anaerobic (lacking oxygen) and nutrient-poor, while sapwood is aerobic (oxygen is present) and richer in nutrients.

Continuing on the theme of remarkable specialization, the researchers found that each tree species harbors its own distinctive microbiome, with microbial communities varying depending on the host species. This is likely due to differences between species in the internal conditions of wood, such as pH, sap flow, phenolic compounds, and the presence of antimicrobial agents. For example, maples, which are known for their sugar-rich sap, had the highest heartwood concentrations of Saccharimonadia, a fermentative, sugar-degrading microbial group. Considering that wood microbial communities appear to be so closely tied to these specific biochemical traits, it raises questions about how their composition might shift over the seasons (e.g., between winter and summer) or vary between trees experiencing different environmental conditions (e.g., drought versus heavy rainfall).

A striking finding by Wyatt and colleagues is that the relatedness of wood-borne microbial communities across tree species mirrored the evolutionary relationships of the trees themselves. This pattern suggests potential co-evolution, with microbial communities adapting to the physiology or biochemistry of their host trees. Similar patterns have been observed in animals. For example, in non-human primates, where phylogenetic relatedness strongly influences gut microbiome composition alongside environmental and dietary factors. Another possibility is that microbes are partially inherited from parent to offspring, causing closely related trees to harbor more similar microbial communities.

In addition to providing insights into the health and resilience of forests, understanding the wood microbiome also opens the door to developing new tools for conservation. Unlike fixed genomes (each tree or human has a single genome that remains largely static) microbiomes are dynamic. Changes in microbial species or the genes they carry can alter how a community interacts with its environment, with significant effects on its host. For example, coral researchers are exploring ways to enhance corals’ microbial communities to boost heat tolerance, potentially providing hope for reef survival under climate change. Similarly, by understanding the microbial communities of trees, and especially in wood which is the largest portion of their biomass, we may discover strategies to help protect trees against disease and support their growth in the face of a rapidly changing environment. For example, interventions like prebiotics or probiotics for trees could one day be used to help vulnerable, high-priority populations withstand devastating diseases such as beech bark disease, whose incidence is rising due to climate change. By studying the wood microbiome, we can better understand the ecological and physiological processes that sustain trees and support forests, providing a foundation for informed conservation strategies.

Study :

Arnold, Wyatt, et al. "A diverse and distinct microbiome inside living trees." Nature (2025): 1-10.