A diverse and distinct microbiome inside living trees

Wyatt Arnold, Jonathan Gewirtzman (), Peter A. Raymond, Marlyse C. Duguid, Craig R. Brodersen, Cade Brown, Naomi Norbraten, Qespi T’ika Vizcarra Wood, Mark A. Bradford and Jordan Peccia ()
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Wyatt Arnold: Yale University
Jonathan Gewirtzman: Yale University
Peter A. Raymond: Yale University
Marlyse C. Duguid: Yale University
Craig R. Brodersen: Yale University
Cade Brown: Yale University
Naomi Norbraten: Yale University
Qespi T’ika Vizcarra Wood: Universidad Nacional de San Antonio Abad del Cusco
Mark A. Bradford: Yale University
Jordan Peccia: Yale University

Nature, 2025, vol. 644, issue 8078, 1039-1048

Abstract: Abstract Despite significant advances in microbiome research across various environments1, the microbiome of Earth’s largest biomass reservoir—the wood of living trees2—remains largely unexplored. Here, we illuminate the microbiome inhabiting and adapted to wood and further specialized to individual host tree species, revealing that wood is a harbour of biodiversity and potential key players in tree health and forest ecosystem functions. We demonstrate that a single tree hosts approximately one trillion bacteria in its woody tissues, with microbial communities distinctly partitioned between heartwood and sapwood, each maintaining unique microbiomes with minimal similarity to other plant tissues or ecosystem components. The heartwood microbiome emerges as a particularly unique ecological niche, distinguished by specialized archaea and anaerobic bacteria driving consequential biogeochemical processes. Our findings support the concept of plants as ‘holobionts’3,4—integrated ecological units of host and associated microorganisms—with implications for tree health, disease and functionality. By characterizing the composition, structure and functions of tree internal microbiomes, our work opens up pathways for understanding tree physiology and forest ecology and establishes a new frontier in environmental microbiology.

Date: 2025
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DOI: 10.1038/s41586-025-09316-0

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