Armillaria is a genus of filamentous fungi within the phylum Basidiomycota, and comprises 40 species. Species are found globally in both temperate and tropical regions, with some species having a limited geographical range whist others are more widespread. As as soil-borne fungus, Armillaria spp. can act as saprophytes/parasites or pathogens, depending on host species and substrate availability. As a phytopathogen, Armillaria is a facultative necrotroph, causing necrosis of the living tree tissue of a variety of host species. Tree declines arise from a combination of biotic and abiotic factors. In oak, Armillaria species are one of those biotic factors, acting either as primary or secondary pathogens. The events that lead to decline act sequentially, or in parallel, and are often unknown, and Armillaria infection is assumed to occur after a primary pathogen or predisposing factor. However, the function of Armillaria species within oak declines is poorly understood, and in particular, it’s activity as a saprophyte or pathogen of oak has barely been studied.
In this work, a combination of isolation studies, molecular identification, rapid diagnostic development, field-based analyses on the ecology and interactions of Armillaria with oak, and contemporary metatranscriptome sequencing was applied to characterise the role of Armillaria spp. in oak declines. First, methodological approaches were optimised for the rapid isolation and growth of Armillaria spp., and subsequent DNA extraction, inhibitor removal and PCR- based analysis of Armillaria phylogenetic marker genes. These approaches formed the basis for the development and validation of a High Resolution Melt curve (HRM)-based rapid diagnostic for Armillaria spp.
Subsequently, these approaches were applied in an ecological study of the interactions of Armillaria spp. with native oak in Chestnuts Wood, Forest of Dean, where Armillaria spp. are having a significant impact on tree health. A. gallica was the only species isolated from the study site and was observed as both a pathogen and saprophyte of oak trees, colonising both asymptomatic and symptomatic oak trees. Symptomatic trees were shown to have less buttress roots than asymptomatic trees, which is a potential predisposing factor to disease that could represent a quick tool to identify at risk trees. Soils within 1 m of symptomatic tree were shown to have significantly greater moisture content, suggesting that Armillaria
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infection induced root malfunction and reduced the trees ability for water uptake.
RNAseq analysis identified significantly up-regulated Armillaria genes associated with fungal pathogenesis in symptomatic tree lesions; CP protein, serpin, and Ubiquitin (although one ubiquitin homologue was down-regulated). This work has highlighted that Armillaria acts as a pathogen on trees at this site, and the severity of infection varies. Manion (1981) described the decline disease model, where the cumulative effect of biotic and abiotic factors causes a decline spiral that amplifies disease. The data from this thesis support this model, highlighting a continuum of tree health status from asymptomatic to symptomatic. The presence of A. gallica on asymptomatic trees also indicates that it is broadly distributed and associated with oak at this site, as both saprophytes and pathogens. It is unclear whether there are separate saprophytic and pathogenic Armillaria strains present on the site, or if the switch to pathogenesis is triggered by abiotic and biotic cues.