Engineering the oak microbiome to combat tree disease

Abstract

Acute Oak Decline (AOD) affects both native oak species (Quercus robur and Q. petrea) in the UK. The disease is characterized by outer bark cracks, dark-fluid weeping patches, D-shaped exit holes produced by the two-spotted buprestid Agrilus biguttatus and necrotic tissue in the inner bark. Tissue necrosis is mediated by a group of bacteria including Brenneria goodwinii, Gibbsiella quercinecans and Rahnella victoriana, which dominate AOD-affected tissue and have the genomic capability to cause plant tissue necrosis. Plant-associated microbiomes can provide beneficial properties to their host, including resistance to abiotic and biotic stresses, priming of host immune system and plant pathogen protection. Increasing evidence in agricultural plants demonstrate that manipulating microbial communities and steering them towards desired phenotypes is a promising strategy for plant disease management. However, progress in this field has been limited for long-lived plant species with ecological and cultural importance. Synthetic microbial communities (SynComs) are one of the approaches of microbiome engineering. SynCom assembly depends on the
availability of strains representing the diversity and functional potential of natural microbial communities. Therefore, microbial isolation studies remain fundamental for plant microbiome engineering. The aim of this work was to engineer the oak microbiome to combat pathogenic bacteria associated with AOD. To achieve this, the objectives of this work were (1) to evaluate microbial
isolation methods to obtain cultures of the oak microbiota, (2) to produce a microbial culture collection from oak samples and identify strains with pathogen-suppressive properties against AOD-associated bacteria; and strains potentially associated to tree health; and (3) to test SynComs to engineer the oak microbiome for suppression of AOD-associated bacteria. In chapter 2, the isolation methods agar plating and dilution-to-extinction were compared for
isolating the oak microbiota. Colony counts and characterization of bacterial and fungal isolates by 16S rRNA gene and ITS sequencing, respectively, showed that the number, richness and composition of isolates was influenced by media composition, aerobic/anaerobic incubation and type of inoculum. Each method captured a different fraction of the microbiota, and only 12 % of the amplicon sequencing variants (ASVs) were detected in both methods, suggesting that both isolation strategies are required to obtain higher taxonomic richness. In chapter 3, a large microbial culture collection of the oak microbiota was produced and screened for pathogen suppressive properties against the AOD pathogens Brenneria goodwinii, Gibbsiella quercinecans and Rahnella victoriana, revealing 341 isolates able to suppress at least one of the target bacteria. Furthermore, 331 isolates associated with the ‘healthiest’ oak trees (based on the lowest phenotypic decline index) were identified. Overall, selected isolates represented 96 bacterial species with potential roles in supporting tree health. In chapter 4, a set of 40 randomly assembled SynComs with different taxonomic richness were tested in vitro against fluorescently labelled strains of B. goodwinii and G. quercinecans, demonstrating strong suppressive effects on both AOD-associated pathogens. Three SynComs were evaluated in inoculation trials using 2-year-old oak seedlings and oak logs for suppression of wild-type strains of B. goodwinii and G. quercinecans. Two SynComs applied before inoculation with the pathogens consistently demonstrated suppressive activity in planta. Overall, these results provided proof-of-concept for the ability of engineered microbiomes to suppress tree pathogens and contribute to disease resistance.

Date of Award	25 Nov 2025
Original language	English
Awarding Institution	Bangor University
Supervisor	James McDonald (Supervisor) & Peter Golyshin (Supervisor)