Britain’s oak trees are dying, and the microbes living inside them may hold the key to their survival. The problem is Acute Oak Decline, a complex disease that kills native British oaks. Unlike a simple infection caused by one pathogen, this decline involves a whole community of harmful microbes—a “pathobiome”—that shifts the tree’s internal ecosystem from healthy to diseased. Current approaches treat one pathogen at a time, but that misses the bigger picture. This project proposes a landscape-scale analysis of the oak microbiome and metabolome—the full collection of microbes and chemical compounds in healthy and diseased trees—to understand how the tree, its microbes, encountered pathogens, and the environment interact to drive health or disease. If successful, the research could lead to engineered microbiomes: custom communities of beneficial microbes that suppress disease and boost the tree’s fitness. This is an emerging frontier in forest microbiome engineering, analogous to precision medicine for humans. The immediate impact would be a new tool to protect a keystone species and the ecosystem services it provides—carbon storage, flood regulation, and habitat for wildlife. The work is applied, but it also advances fundamental understanding of how complex microbial communities govern plant health, a question with implications for agriculture and forestry far beyond oaks.
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Tree declines caused by climate perturbation, anthropogenic stressors and disease outbreaks have resulted in recent forest mega-disturbances and are a major global concern. Until recently, progress has been hampered by a lack of high-throughput analytical approaches for systems-based analysis of the multidimensional factors that drive declines. Our previous research on Acute Oak Decline, a complex decline disease of native British oak, has highlighted how microbiome shifts to a 'pathobiome', are associated with tree disease. This work challenges the one pathogen = disease paradigm, leading to new hypotheses on the role of microbiomes in health and disease, and highlighting the need to revise classical disease paradigms to include the microbiome. The microbiome is a major determinant of plant health, and we hypothesise that the oak microbiome can be manipulated to improve host fitness and disease suppression. Here, we propose a landscape-scale analysis of the oak microbiome and metabolome in health and disease, to inform the design and validation of engineered microbiomes for disease suppression. Microbiome engineering is an emerging research frontier with many novel applications. The project will address new hypotheses regarding how complex multidimensional interactions between the tree host and its microbiota, encountered pathogens, and the environment, influence host fitness and disease susceptibility. The research will initiate a new frontier in forest microbiome engineering and precision medicine to future-proof iconic tree species and the ecosystem services they provide.
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