Oak has long been affected by episodes of decline, an interaction of multiple factors that reduces host vigour. A wide range of abiotic, insect and pathogenic agents may play causal roles in an outbreak; acting independently, together, or consecutively in a complex process. In Britain a novel form of Acute Oak Decline (AOD) is increasingly reported. Typified by symptoms of stem 'bleeding', bark-splits that weep dark exudate, the stem symptoms overlay patches of necrotic cambial tissue concealed beneath the bark. An initial investigation by Forest Research identified a suite of bacterial species as putative causal agents. Signs of insect activity are frequently found in association with the stem lesions. Galleries are usually present in the conductive tissue and some of the affected trees have distinctively D-shaped exit holes created by the buprestid beetle Agrilus biguttatus. Although declines are typified by complex causes, the dominance of these two organisms (bacteria and beetle) makes understanding their interaction an important step in defining the epidemiology of the syndrome. The current study aims to provide initial investigations into the epidemiology of AOD. By mapping and monitoring trees within eight study sites symptom development was accurately recorded from a reliable baseline. These data give insights into disease development in terms of rate of spread, tree mortality and disease distribution. Repeated monitoring at multiple time points documents the progression of symptoms, within and among trees. Site monitoring is complemented by preliminary studies investigating the role of the buprestid beetle Agrilus biguttatus in the decline complex. By developing trapping methods populations of Agrilus beetles can be monitored in terms of flight period and species composition. The focus on A. biguttatus seeks to confirm whether the larvae present in galleries are A. biguttatus and to investigate the link between beetle, larvae and bacteria.

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Phytophthora ramorum is causing major damage to the economy and the natural ecosystems of the countries where it is found. There are four different lineages of P. ramorum: NA1, NA2, EU1 and EU2. EU2 has only been found in Northern Ireland and southwest coast of Scotland The populations EU1 and EU2 on the island of Ireland were studied. The results showed that all the isolates collected from the Republic of Ireland were EU1, as In the rest of Europe and the majority of the Isolates from Northern Ireland and Scotland were EU2. Further study resulted in phylogenetic trees that suggested that the EU1 population in the Republic of Ireland is the result of multiple introductions brought by plant trade from Europe. Additionally! the EU2 population in Northern Ireland is the results of a single Introduction, probably brought from Asia, and then spread across the country. The interaction of P. ramorum with its most affected host In the UK, larch, was studied. High throughput sequencing was performed with Illumlna 2000 Hiseq in European and Japanese larch trees infected with the lineages EU1 and EU2. This showed a larger number of general defence genes activated in European larch against the pathogen, along with a larger number of Inactivated genes In Japanese larch, supporting the idea that European larch is more resistant to P. ramorum. Some defence molecular pathways were studied, showing that European larch activates more genes in each specific pathway. A selection of genes involved in the different defence pathways were studied showing that the highest peak of plant defence against the pathogen occurs 3 days after the inoculation, suggesting that for the plant It Is important to react quickly in order to survive the pathogen attack.

Concerns over anthropogenic climate change coupled with reduced availability and rising prices of domestic fossil fuels have led a drive towards a low carbon economy and have seen increasing interest from Governments in the development of renewable energy technologies. In 2009, a Government strategy proposed by the Renewable Energies Directive, outlined that by 2020, 15% of the UK’s total energy consumption should come from renewable resources. Part of the initiative in meeting this target, and in helping mitigate greenhouse gas emissions, includes the increased production of energy crops, such as Short Rotation Coppice (SRC) willow (Salix spp.). Although SRC willow cultivation could contribute towards the renewable energies target set for 2020, its growth on a large-scale would result in significant changes to the agricultural landscape. Through employing both an above and below ground approach this thesis demonstrates how the cultivation and management of SRC willow can impact upon locally occurring ecological communities. The conversion of traditional pastoral farming systems to SRC willow is shown to be beneficial for avian communities from a biodiversity perspective, although the thesis highlights the potential for this novel crop to act as an ecological trap for locally breeding species. Furthermore, the results of this research illustrate how changing the management of the SRC willow crops, to facilitate the bioremediation of municipal wastewaters, affect the composition of invertebrate communities that have not previously been studied in this system, and can lead to changes to an essential ecosystem process, decomposition. Together, these findings provide a novel insight into the agro-ecology of commercial SRC willow cultivation.

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