A diverse and distinct microbiome inside living trees

Abstract Despite significant advances in microbiome research across various environments 1 , the microbiome of Earth’s largest biomass reservoir– the wood of living trees 2 – remains largely unexplored. This oversight neglects a critical aspect of global biodiversity and potentially key players in tree health and forest ecosystem functions. Here we illuminate the microbiome inhabiting and adapted to wood, and further specialized to individual host species. We demonstrate that a single tree can host approximately a trillion microbes in its aboveground internal tissues, with microbial communities partitioned between heartwood and sapwood, each maintaining a distinct microbiome with minimal similarity to other plant tissues or nearby ecosystem components. Notably, the heartwood microbiome emerges as a unique ecological niche, distinguished in part by endemic archaea and anaerobic bacteria that drive consequential biogeochemical processes. Our research supports the emerging idea of a plant as a “holobiont” 3,4 —a single ecological unit comprising host and associated microorganisms—and parallels human microbiome research in its implications for host health, disease, and functionality 5 . By mapping the structure, composition, and potential sources and functions of the tree internal microbiome, our findings pave the way for novel insights into tree physiology and forest ecology, and establish a new frontier in environmental microbiology.