A study of the microorganisms colonizing pruning wounds on mature oaks (Querous robur) has been made. The wounds were approximately 8" diameter and the type likely to occur on trees of amenity value in parklands and similar sites, where large limbs have been removed due to their being unsafe, diseased of causing obstruction. There would appear to be a definite succession occurring on oaks. In the initial stage there was a deep blue green discolouration, primarily of the sapwood. Organisms consistently isolated at this stage included species of Penicillium, Aureobasidium, Cladosporium, Trichoderma, Botrytis, Epicoccum, Bacillus and a range of Cram-negative rods. These pioneer colonists ae assumed to have originated from the air. They were characteristic of both the heartwood and sapwood and were isolated from both surface and sub-surface samples. After one month, sporing fungi were visible on the wound face and in some cases associated with intense blusing and bleeding of the exposed face. Successional changes followed the establishment of pioneer celenists and after two months species of Graphium and Phialophora became more prevalent. The next organisms to appear included species of Paecilomyces and representatives of the Sphaeropsidales and Mvcelia Sterilia, Basidiomycetes, particularly Stereum hirsutum did net appear until the wound was 10 months old. Spores of S. hirsutum have been shown to germinate well on elder wound tissue (79% germination rate) but poorly on freshly exposed wound surfaces. Bacteria were cultured frequently from all ages and types of wounds. The steroscan was usod in the microscopic examination of wound tissue. Evidence has been presented for the presence of bacteria, soft rot, white rot and broun rot fungi, and their effects on the tissues. The isolation and Stereoscan work support the idea that non-hymenomycetous fungi and bacteria precede Hymenomycetes in the colonization of pruning wounds on oaks.

The work described in this thesis attempts to determine the degree of retention of essential, non-essential and/or pollutant, trace and minor elements that are taken into a tree's system, in order to evaluate the usefulness of the elemental analysis of tree rings (dendroanalysis) as a means of investigating past environmental conditions. A list of elements that are of interest in such a study, is compiled. The concentrations of many of these elements in a wood matrix can be measured by using the multi-elemental analytical technique neutron activation, which is the method employed for the majority of analyses performed in this work. A brief outline of relevant tree physiology is given; and two sampling techniques, the irradiation conditions and the computer assisted analysis of results, are described. Preliminary results are obtained by determining the concentrations of up to eighteen elements in an elm and an oak tree from the Guildford area, and a cedar tree that had been situated in the suburbs of Reading. Ring by ring variations of many of the elemental concentrations are plotted out, with particular reference to the physiologically different areas in which the growth rings are situated. From these results, and others reported in this thesis, it appears that the natural biochemical processes in a tree can alter some of the original elemental concentrations of the tree rings. A three-dimensional analysis of a second elm from Guildford has been performed, and the results from the two Guildford elms and a third elm tree are compared to evaluate the effects of 'Dutch' elm disease, and an associated secondary infection, on the elemental analysis of elm trees. Four elm trees from Stoke-on-Trent (a city which has had high levels of atmospheric pollution in the past) are analysed and compared with the results from the first Guildford elm. Other methods that might be used for the elemental analysis of tree rings are also investigated, and some suggestions for future work in the field of dendroanalysis, are made.

Legally inhabited indigenous, extractive and sustainable use tropical forest reserves, have been lauded as a solution to the intractable problem of how to assure the welfare and secure livelihoods of the world’s diverse forest-dependent people, whilst conserving the world’s most biodiverse terrestrial ecosystems. This strategy has been critiqued by human rights advocates, who assert that legally inhabited reserves paternalistically restrict the livelihood choices and development aspirations of forest-dwellers, and by conservationists, who argue that sustained human presence and resource extraction erodes tropical forest biodiversity. This thesis examines both the anthropogenic impacts on tropical forests at the regional, landscape and household scales and the livelihood challenges faced by semi-subsistence local communities in the Brazilian Amazon. A spatially explicit dataset of 633,721 rural Amazonian households and an array of anthropogenic and environmental variables were used to examine the extent and distribution of structural (deforestation) and non-structural (hunting) human disturbance adjacent to 45 cul-de-sac rivers across the Brazilian states of Amazonas and Pará. At the landscape and household scales, a total of 383 camera trap deployments, 157 quantitative interviews and 164 GPS deployments were made in the agricultural mosaics and forest areas controlled by 63 semi-subsistence communities in the Médio Juruá and Uatumã regions of Central-Western Brazilian Amazonia, in order to quantify and explicate the (i) livelihood costs incurred through the raiding of staple crops by terrestrial forest vertebrates, (ii) degree of depletion that communities exert upon the assemblage of forest vertebrates and (iii) spatial behaviour of hunting dogs and their masters during simulated hunts. Our results indicate that at the regional scale, accessibility, fluvial or otherwise, modulated the drivers, spatial distribution and amount of anthropogenic forest disturbance. Rural household density was highest in the most accessible portions of rivers and adjacent to rivers close to large urban centres. Unlike the low unipolar disturbance evident adjacent to roadless rivers, road-intersected rivers exhibited higher disturbance at multiple loci. At the household and landscape scales semi-subsistence agriculturalists lost 5.5% of their staple crop annually to crop raiders and invested significant resources in lethal and non-lethal strategies to suppress crop raiders, and to avoid losses an order of magnitude higher. Crop raiding was heightened in sparsely settled areas, compounding the economic hardship faced by communities already disadvantaged by isolation from urban centres. A select few harvest-sensitive species were either repelled or depleted by human communities. Diurnal species were detected relatively less frequently in disturbed areas close to communities, but individual species did not shift their activity patterns. Aggregate species biomass was depressed near urban areas rather than communities. Depletion was predicated upon species traits, with large-bodied large-group-living species the worst impacted. Hunting dogs travelled only ~ 13% farther than their masters. Urban hunters travel significantly farther than rural hunters. Hunting dogs were recognised to have deleterious impacts on wildlife, but were commonly used to defend against crop raiders.

The overall aim was to gain information required for improvement of wood quality in British oaks (Quercus robur and petraea). Specific aims were 1) to investigate the nature and incidence of shake in British oaks; 2) to quantify variations in oak wood structure and properties, identifying which characteristics are under genetic control and which associated with growth rate; 3) to make prescriptions for selection and silviculture of oak, with a view to improving wood quality in future British crops. Site surveys (including soil analyses) of 42 woodlands were carried out. An index of severity was devised to standardise shake assessment within individual trees. Wood structure was analysed in oaks from shake-prone and sound woodlands. Associations of wood structure and property variations with genotype and growth rate were analysed in oaks from a seed origin trial. Environmental factors were strongly associated with shake. High shake incidence occurred on sites which gave poor rooting conditions for oak: shallow, nutrient poor soils with low clay content and low calcium availability, and with soil texture and/or site topography leading to seasonal droughtiness or waterlogging. Woodland type (shake-prone or sound) was a stronger influence than tree condition (shaken or sound) on wood structure: oaks from shake-prone woodlands had wider rings, smaller earlywood percentage, larger wide rays and larger earlywood vessel radial diameters. Density, sapwood width, earlywood vessel frequency and proportions of wide rays and of latewood vessels and fibres varied between seed origins; these variables therefore have selection potential for improvement of oak wood quality. Many parameters also varied with growth rate, and earlywood vessel radial diameter was strongly associated with current ring width. A model of shake development is proposed in which various predispositions (structural weaknesses) and triggers (mechanical stresses) influence a tree over time. It is proposed that predispositions are caused by environmental factors at the time of wood formation, resulting in physiological stress or cambial damage. Genotype may modify response or susceptibility to environment. Predispositions may be extended by secondary weakening. Triggers of shake are thought to be natural internal growth stresses supplemented by the action of external forces (such as wind). Recommendations are made for site choice and silviculture of future British oak crops.

Habitat loss and climate change are two of the most important threats to biodiversity in the tropics. The climate mechanism to Reduce Emissions from Deforestation and forest Degradation (REDD+) can therefore, in theory, address both of these threats by funding forest conservation and slowing climate change. However there are concerns that, if not properly planned, REDD+ could in practice negatively impact biodiversity. In this thesis I introduce the emergence of biodiversity concerns in REDD+ and the relevant safeguards developed at the international negotiations. I present a conceptual framework for understanding opportunities and risks for biodiversity in REDD+, bringing together the literature on biodiversity co-benefits and safeguards. In the last seven years, REDD+ went through a readiness phase and was piloted in over 300 subnational initiatives across the tropics in preparation and anticipation for inclusion in the future global climate regime. I assess 22 of these REDD+ initiatives located in six countries and explore how biodiversity considerations are incorporated into the project design and the challenges faced in delivering biodiversity co-benefits. Many project developers demonstrated strong intentions to safeguard biodiversity, only a handful had explicit goals and interventions targeting biodiversity conservation; often citing the lack of capacity and incentives to protect biodiversity as challenges. I then focus on Indonesia where I use spatially explicit methods to explore the relationship between carbon and biodiversity and the potential for 1st generation REDD+ initiatives to deliver biodiversity benefits. I show that carbon and biodiversity are not correlated in Indonesia; while REDD+ initiatives tend to be (perhaps surprisingly) located in forests important for biodiversity, these are not necessarily the most threatened by future deforestation, thus limiting the contribution of REDD+ to conservation. I then focus on two newly approved subnational REDD+ initiatives and explore how the challenges in implementing REDD+ (especially the slow approval process and reduction in the proposed project area) have impacted orangutan conservation. I show that the Indonesian government will have to re-assess the way in which REDD+ projects are currently being approved if it is serious about its commitments toward orangutan conservation and emission reduction. This study strengthens the notion that REDD+ has the potential to deliver huge benefits for tropical forest biodiversity, especially when located forests most threatened to deforestation. However, progress of REDD+ at the international negotiations have been slow and its inclusion as part of the future climate regime is still uncertain in spite of the urgency of climate change and the potential irreversible negative implications a failed global REDD+ mechanism will have on climate, people and biodiversity.

The thesis has two objectives. The first is to describe the vegetation in the State of Sabah. To this end all available knowledge has been examined and a classification scheme outlined based on ecological considerations. A more detailed classification of the dipterocarp forests into Types based on the relative abundance of big tree species is presented. The second objective is the development of management criteria to achieve satisfactory natural regeneration following logging in the dipterocarp forests and to enhance growth rates. An account is given of the dynamic Processes in the natural forest which lead to the replenishment of the species and this is followed by an examination of silvicultural treatments designed to influence the success of natural regeneration. Climber cutting and tree marking prior to felling are suggest`, ', as being useful in restricting the amount of damage done to the forest, particularly to soil and seedlings. After felling selective removal of unwanted species where these are likely to interfere with the growth of regeneration is advocated and a further intervention is recommended at 10-15 years 3tfter felling. Assessment techniques designed to measure desirability of treatment are discussed and preliminary results from yield plots are presented. Providing silvicultural treatments are undertaken it is estimated that second cuts in these forests may be taken at 60 years after felling. The stands will be essentially of the same suecies though refinement will have eliminated many of the AN less desirable timbers, and growth rates suggest that trees of the genus Shorea (section Rubroshorea) will be of most importance in the second growth stands.

Integrated pest management calls for new biocontrol solutions in management of forest diseases. Endophytic fungi that are commonly found in tree tissue may have potential in biocontrol. However, the links between endophyte status and disease tolerance are still unclear, and we know little about the mechanisms by which the endophytes can influence tree pathogens. The first goal of the thesis was to compare the endophyte status in elm (Ulmus spp.) trees with low vs. high susceptibility to Dutch elm disease (DED), caused by Ophiostoma fungi, and to find correlations between endophytes and the susceptibility pattern of the trees. The second goal was to investigate the potential mechanisms of antagonism by the endophytes towards the pathogen. Thus, endophytes were isolated from leaves, bark and xylem of elms that differed in DED susceptibility. The isolates were screened for their potential to counteract the pathogen in dual cultures. Selected strains were investigated using Phenotype MicroArrays to obtain the substrate utilization profiles that reflect the endophytes’ ability to compete with the pathogen for a nutritional niche. To test for a protective effect against the disease, promising isolates were injected into young elms. Preliminary analyses were done to identify the extracellular chemicals that some of the endophytes released into the growth medium. The results showed that the frequency and diversity of endophytes was higher in xylem of elms with high susceptibility to DED. Some endophytes deadlocked the pathogen with extracellular chemicals in vitro, while others had a faster growth rate. Several endophytes were able to utilize substrates more effectively than the pathogen. A preventive treatment with endophytes protected elms against DED, but the effect was unstable across years. Bioactive fungal extracts had a complex chemical profile, and the individual compounds in the extracts remain to be identified. Because endophytes antagonized the pathogen through different mechanisms, I suggest that an endophytebased biocontrol of DED could be best achieved through a synergistic effect of several endophyte strains.

Acute Oak Decline (AOD) is a complex Decline-disease affecting both native species of oak within the United Kingdom. Two novel species of bacteria, Gibbsiella quercinecans and Brenneria goodwinii, have been consistently isolated from necrotic lesions of AOD affected trees and are apparently absent from healthy oak trees. The aim of this thesis was to determine the role of Gibbsiella quercinecans and Brenneria goodwinii in AOD via the application of molecular methods. The first step in this investigation was to identify an appropriate molecular marker to differentiate between closely related oak lesion isolates belonging to the family Enterobacteriaceae. Using ITS1 profiling, a set of Enterobacteriaceae strains, primarily G. quercinecans and B. goodwinii were resolved, and eight strains were selected for sequencing to draft level. This enabled characterisation of strain level variation between sequenced isolates and functional annotation of genome encoded virulence factors, revealing an assortment of phytopathogenic virulence genes As the isolates were sequenced to draft level and no other whole genome sequences of G. quercinecans or B. goodwinii existed, the type strains of both species, i.e. G. quercinecans FRB97 and B. goodwinii FRB141 were sequenced to completion using the Pacific Biosciences RSII sequencing platform. The second component of this investigation characterised the putative phytopathogenic behaviour of G. quercinecans and B. goodwinii. Data collected from whole genome sequencing was used to align metagenomic and metatranscriptomic data recovered from the necrotic lesions of AOD affected trees, and to inform transcriptomic analysis of virulence gene expression within in vitro cultures containing oak tissue. The analysis demonstrated that G. quercinecans and B. goodwinii alter their behaviour in the presence of oak tissue, and active functionality of G. quercinecans and B. goodwinii within necrotic lesions AOD-affected trees. These experiments describe the first whole genome and transcriptome characterisation of G. quercinecans and B. goodwinii.

Obtaining quantitative information about the recovery of fire affected ecosystems is of utmost importance from the management and decision-making point of view. Nowadays the concern about natural environment protection and recovery is much greater than in the past. However, the resources and tools available for its management are still not sufficient. Thus, attention and precision are needed when decisions must be taken. Quantitative estimates on how the vegetation is recovering after a fire can be of help for evaluating the necessity of human intervention on the fire-affected ecosystem, and their importance will grow as the problem of forest fires, climate change and desertification increase. This thesis presents a comparison of methods to extract quantitative estimates of vegetation cover regrowth in burned areas with remote sensing data. In order to eliminate possible sources of error, a thorough pre-processing was carried out, including a careful geometric correction (reaching RMSE lower than 0.3 pixels), a topographic correction by means of a constrained Minneart model and a combination of absolute and relative atmospheric correction methods. Pseudo Invariant Features (PIF) were identified either by visual inspection methods or by a new automated selection method based in temporal Principal Component Analysis (PCA), which has been called multi-Temporal n-Dimensional Principal Component Analysis (mT-nD-PCA). This automated method demonstrated its capability in selecting accurate and objective PIFs within the satellite images. Spectral Mixture Analysis (SMA) was compared against quantitative vegetation indices which are based on well known traditional vegetation indices like Normalised Difference Vegetation Index (NDVI) and Modified Soil Adjusted Vegetation Index (MSAVI). Accuracy assessment was performed by regressing vegetation cover results obtained with each method, against field data gathered during the field work campaigns. Results obtained showed how vegetation cover fractions obtained with the NDVI based quantitative index were the most accurate, being superior to the rest of the techniques applied, including SMA.

Scottish forestry policy promotes integrated multifunctional forestry and continued forest expansion, and the private forestry sector is key to achieving these goals. However, a variety of factors can constrain multifunctional forestry, particularly in upland areas. Management objectives for private forests are also not always widely known and the potential impacts of government policy, and particularly conservation designations, on the delivery of multifunctional forestry have not been explored. Furthermore, the effects of landownership on forest management are unclear. The key aim of this research was to evaluate how forests and woodlands in the Cairngorms are being managed, and to determine the main constraints and opportunities to the further application of a multifunctional approach to forest management in the region at various scales. The research incorporated GIS analysis, a postal questionnaire survey and semi-structured interviews. A typology was developed which identified three key management themes: sustainable multifunctional management; restricted functionality forestry; and dual function management. Forest owner preferences, economic concerns, government policy and the wider land use context all influence forest management. No consistent relationship was evident between specific types of landownership and forest management functionality. A link was apparent between species and structural diversity and forest multifunctionality. Overall, ‘social’ objectives were relatively weak, particularly for private forests, while ‘environmental’ objectives were consistently strong and ‘productive/economic’ objectives varied in importance. The themes of constraint and opportunity were: spatial fragmentation and integration; forestry markets; bureaucracy and policy integration; public pressure and public support; and unpredictability and forest resource resilience. Many constraints result from temporal, spatial and organizational scale mis-matches between social and natural systems. The matching up of scales at the management, organizational and market levels and the treatment of forests as complex social-ecological systems is recommended. Further recommendations include: further land management integration; increased policy regionalization; timber market localization; and enhanced long-term planning.