Investigating the influence of environmental change on the oak microbiota and the development of Acute Oak Decline

Abstract

Plant microbiomes are integral components of plant health and ecosystem functioning, significantly influencing plant physiology, disease resistance, and nutrient acquisition. Previous research into manipulating plant microbiomes has shown great potential in enhancing agricultural yields and combating plant diseases in food crops and non-woody plant systems. However, our understanding of microbiome dynamics in large, long-lived tree species is limited, representing a critical knowledge gap. This is particularly concerning, given the escalating threat of widespread tree declines, which are often exacerbated by environmental stressors. One such decline is Acute Oak Decline (AOD), a complex decline disease that threatens native oak species in the UK, where abiotic stressors, such as drought, are thought to play a crucial role in its predisposition. Bacterial inner bark tissue necrosis is a major symptom of AOD; however, the precise mechanisms that enable these pathogens to thrive and trigger rapid decline in oak trees remain unclear. Emerging evidence suggests that the oak microbiome may play a crucial role in the development of AOD symptoms. However, a critical gap in our understanding lies in how oak microbiomes respond to abiotic stressors, such as drought, and how these responses subsequently influence oak health and its vulnerability to AOD development. This thesis seeks to unravel the complex interactions between oak microbiomes, environmental stressors, and disease susceptibility.

This thesis begins by reviewing the literature on global tree declines, Acute Oak Decline, tree microbiomes, the influence of abiotic stressors on microbial communities, and common methods used in tree microbiome studies (Chapter 1). Chapter 2 addresses a common issue in oak (host) chloroplast and mitochondria co-amplification in bacterial single-gene amplicon sequencing studies, which we encountered during preliminary experiments. This issue was successfully overcome by the design and validation of Peptide Nucleic Acid (PNA) clamps. PNA clamps were subsequently used in a large-scale woodland experiment where 144 oak trees were subjected to rain exclusion (to limit water
availability) and ringbarking (to disrupt vascular systems) and inoculated with biotic agents associated with Acute Oak Decline. Samples of leaf, inner bark tissue, and roots (rhizosphere) were collected at four distinct time points over a two-year period. This allowed us to track the microbiome shifts, starting from the baseline of healthy trees (Chapter 3), through the effects of the abiotic treatments (Chapter 3), and ultimately as AOD symptoms developed in predisposed trees (Chapter 4).

This work revealed a remarkable resilience of the bacterial and fungal microbiome communities in mature Quercus petraea trees to short-term abiotic and biotic stresses. While alpha and beta diversity analyses revealed the overall bacterial and fungal community structures remained relatively stable, a fine-scale analysis of abundance changes revealed patterns. Root microbiomes responded to rain exclusion by enriching Actinobacteria, suggesting their potential as a biomarker. Additionally, potential plant-growth-promoting bacteria (Nocardia, Actinomycetospora) were also enriched, likely driven by changes in root exudation. In contrast, following rain exclusion, the inner stem microbiome exhibited a reduction in potentially beneficial bacteria and an increase in potentially tree-saprotrophic and pathogenic fungi, which could increase the oaks' vulnerability to AOD.

Oak trees experiencing both ringbarking and AOD symptoms exhibited an increase in acid-tolerant bacteria (Acidibacter, Acidicapsa) in the inner stem, indicating that the environment is becoming increasingly acidic. The root/rhizosphere of AOD symptomatic trees revealed an increase in Armillaria, a fungus commonly associated with oak decline. Additionally, the combined impact of AOD symptoms and rain exclusion also increased the abundance of potentially pathogenic and wood-saprotrophic fungi (Melanconis, Hyaloscypha).

These results suggest that the oak microbiome may be shifting to become less supportive of tree health, potentially increasing its vulnerability to AOD. Future research should investigate the functional roles of the identified microorganisms in this study to gain a deeper understanding of these changes, particularly in the understudied stem endophytic microbiome.

Date of Award	14 Aug 2025
Original language	English
Awarding Institution	Bangor University
Sponsors	Kess II East, Woodland Heritage Limited, BBSRC (BB/I007091/1) & NERC
Supervisor	James McDonald (Supervisor) & Amy Ellison (Supervisor)