Understanding the critical roles of bacteria and fungi in oak health and disease

At Bangor University we have been working for almost ten years in collaboration with Forest Research, and other institutions in the UK and beyond, to understand the role of both beneficial and pathogenic microbes in oak health and disease.

Our native oaks are under serious threat from several diseases such as Acute Oak Decline (AOD) and Chronic Oak Decline (COD), in addition to new and emerging threats that are currently under investigation. Most diseases affecting oak have complex causes that include combinations of abiotic (environmental) and biotic (pest and pathogen) stressors that weaken the host and ultimately lead to disease development and expression.

The plant microbiome (the collection of plant-associated microorganisms and their encoded genes) is a major determinant of health and productivity, for example, by promoting nutrient availability, resistance to environmental stresses, and defence from pests and pathogens.

Tree microbiomes therefore have a significant influence on tree fitness and phenotype. However, until recently, the analytical tools to study the millions of oak-associated microorganisms and their genes were not available, and consequently, the composition and function of oak microbiomes was poorly understood.

With generous support from Woodland Heritage and DEFRA, we have been using pioneering new DNA sequencing technologies to study the oak microbiome.

Initially focussing on Acute Oak Decline, we used these new DNA sequencing technologies to sequence the microbiome of healthy trees, and trees with AOD lesions, to provide evidence of key causal bacteria associated with lesion formation_1,2.

We were also able to sequence the genome of these bacteria, that had been isolated into pure culture and taxonomically described by colleagues at Forest Research and the University of West England, to understand their mechanisms of pathogenicity₃ which can then be validated using laboratory experiments.

We are now using these methodologies to continue our study of the role of the microbiome in AOD, in addition to characterising chronic oak declines caused by fungal root-rot pathogens such as Armillaria honey fungus, and other canker diseases.

These approaches enable us to identify the specific bacterial and fungal species associated with health and disease, and by studying which genes and functions they encode, enables us to assess their activity under different conditions. Understanding the role of the tree microbiome in health and disease, and harnessing the microbiome to promote disease suppression, may therefore represent important tools in our fight to future-proof our iconic native oak.

James McDonald, Bangor University

_{1.    Denman, S. et al. Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline. ISME J. 1–14 (2017). doi:10.1038/ismej.2017.170
2.    Broberg, M., Doonan, J., Mundt, F., Denman, S. & McDonald, J. E. Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. Microbiome 6, 21 (2018).
3.    Doonan, J., Denman, S., Pachebat, J. A. & McDonald, J. E. Genomic analysis of bacteria in the Acute Oak Decline pathobiome. Microb. Genomics (2019). doi:10.1099/mgen.0.000240}