The present work is the first report of the Multi Locus sequence typing (MLST) of the B. thuringiensis strains isolated from the phylloplane of the clover leaf. A clonal population structure was indicated, although greater variation in sequence types (STs) was discovered in previous collections of B. cereus/B. thuringiensis. The three techniques of DGGE, T-RFLP and MLST were compared for the first time to judge whether the fingerprinting and typing techniques provide the same level of resolution in the structure of the bacterial communities. The techniques resulted in interesting findings: (a) the clustering of fingerprints correlated with the time of collection; (b) there was variability in the T-RFLP profiles, possibly due to the choice of restriction enzymes used in the study; (c) the rpoB gene gave better resolution in DGGE than 16S rDNA; and (d) DGGE types detected ambiguities in the nucleotides. The project is the first report of experiments to study natural colonisation of a plant by B. thuringiensis, causing a pathological effect on a susceptible insect. The pathogenic effect or interaction of Bt naturally colonising Brassica plants on neonate larvae of Pieris brassicae has been achieved. Initial screening studies of B. thuringiensis from the Antarctica have been completed. The two most important genes coding for the toxins cry1 and cry2 have been amplified and the sequences have been submitted to the NCBI database. The strains from Antactica have also been screened for the nematicidal and enterotoxic toxins. The Antarctic B. thuringiensis strains have been found to possess large and irregular shaped crystals. The sub lethal and lethal effects of crystal preparations from Antarctic B. thuringiensis isolates on Orchesella cincta, Folsomia candida and Seira domestica has been achieved, showing moderate level of toxicity against these springtails.

Plant cells require considerable transcriptional reprograming to mount an effective response to pathogens. Plant responses to pathogens have to be finely balanced with other vital biological processes such as development and growth. A major mechanism controlling the modulation of gene expression is chromatin remodelling. Chromatin remodelling requires histone covalent modifications and/or the action of ATP- dependent remodelling complexes. The combined action of these determine the accessibility of transcription factors and the basal transcription machinery to DNA and therefore greatly impact gene expression. There are several examples of histone modifying and chromatin remodelling enzymes previously shown to regulate plant development and immunity. This thesis explored the role of chromatin in plant defences, and how chromatin remodelling forms an integral part of the defence response. Chapter 1 aimed to discover a “hidden” signal of chromatin marks in plant defence-responsive genes using an array of bioinformatics techniques. Subsequently, histone H3K27 tri- methylation (H3K27me3) was identified as a mark associated with gene repression at defence-related loci. The role of histone H3K27me3 and its associated histone demethylase enzymes REF6 and ELF6 were empirically characterised. Chapter 2 is dedicated to a reverse genetics screening investigating the role of the chromatin remodelling ATPases Arabidopsis family in plant defences, and describes the most prominent phenotypes. And lastly, Chapter 3 dissects in greater detail the role of the chromatin remodelling ATPase EDA16 in plant defence. Pathogen assays, RNA-seq and other molecular techniques suggest that EDA16 is a negative regulator of immunity induced upon pathogen perception to regulate the amplitude of defence responses.

Phytopathogens have developed methods to suppress, manipulate and avoid host defences though the production of toxins and proteins that act on the exterior and interior of host cells. Pathogenic proteins that promote susceptibility to the pathogen are termed effectors, and can function through the suppression of host defences and the diversion of host nutrients. Plants are able to detect select effectors, and thus regain resistance. This multilayered defence response and diverse array of pathogenic effectors can cause the outcome of infection to be decided by a single protein from either organism. Current characterised effectors are able to block pathogen-associated molecular pattern recognition, downstream signalling, up-regulate susceptibility genes including nutrient transporters, modify chromatin structure, interfere with RNA metabolism, suppress or prevent effector-triggered immunity and block the defensive and culminating plant cell death. Research conducted here aims to investigate the in uence of effectors from two pathogens upon transcription in their common host, Arabidopsis thaliana. Over 30 Pseudomonas syringae pv. tomato (Pst) DC3000 effectors, which are delivered directly into the host cell, have been at least partially characterised with several more predicted from the sequenced genome. The research presented here analyses a high resolution microarray time series dataset, comparing the transcriptional events that take place during virulent Pst DC3000 infection to infection with an avirulent mutant that is unable to deliver effectors into the host cell; Pst HrpA

The Arbuscular Mycorrhizal (AM) fungi are a group of obligate plant root endosymbionts, which form associations with an estimated two thirds of terrestrial plant species. Their extra-radical mycelium extends throughout the soil and absorbs nutrients that are transferred to their host plant in exchange for a purely phytogenic carbon supply. Due to their ubiquity and their functional importance, they are the subject of much research into their community ecology, yet much is still unknown. For instance: whether or not AM fungi display preference for certain host plant species; how environmental heterogeneity and energy availability affect communities; and the relative influence of niche and neutral processes. This thesis describes experiments which profile AM fungal communities and environmental properties of their habitat at different spatial scales in different plant species. Network analysis revealed patterns indicative of niche-based processes structuring AM fungal communities more than neutral processes, phenotypic trade-offs between AM fungi, and of priority effects influencing diversity and unevenness. Difference between plant species in the heterogeneity of surrounding soil was dependent on spatial scale. The effect of decreased carbon allocation on AM fungal communities is greater in more heterogeneous habitats. These results suggest that the detection of host plant preference in AM fungi is dependent on spatial scale of sampling, driven by interspecific variation in plant root architecture, soil physical properties and AM fungal vital rates.

Atmospheric CO2 levels have been increasing at an accelerated rate for the last 250 years, much of which is absorbed by the oceans, resulting in a process called ocean acidification (OA). This phenomenon has the capacity to disrupt many marine biological processes that utilise carbon, in particular photosynthesis and calcification, and as such phytoplankton have been a main topic of OA studies. While research has accelerated over the last decade, establishing general trends still remains confounded by methodological inconsistencies. Coccolithophores, particularly the species Emiliania huxleyi, are both ecologically and biogeochemically important phytoplankton; however, one strain (NZEH) has produced highly varied results. Here, we present a multivariate analysis that suggests previous inconsistencies between past studies of NZEH may be driven by variance of the light:dark (L:D) cycle used for growth. Experimental analysis on NZEH showed that under a 14:10h L:D cycle, CO2 induces significantly slower growth rates and higher PIC and POC cell-1, but this effect is dampened under 24h of light. This was widened to encompass more taxa, including more isolates of E. huxleyi (PLY70-3, PLY124-3, RCC962), and two other species of coccolithophore; Gephyrocapsa oceanica and Coccolithus pelagicus. L:D cycle changed the observed OA response, with two main responses divided by biogeographical origin. In tropical taxa, 24h light enhanced the effects of increased photosynthesis, but dampened the decrease in calcification in response to CO2. For temperate taxa, 24h dampened both the increases in photosynthesis and calcification with CO2. Evaluation of photobiology reveals that both CO2 and longer photoperiods induce a “high light” acclimation response, and changes in coccosphere thickness suggest it has a photoprotective role. Finally, results from bioassay experiments on natural phytoplankton populations in the polar regions show that CO2 response is hard to predict and based on community composition and ambient starting conditions. This work serves to further highlight the importance of environmental variables that moderate the OA response in accurately understanding future biogeochemical cycles. Future models attempting to predict the impact of OA upon marine systems must critically account for interactive role of light availability.

Crop wild relatives are important for agriculture due to the genetic richness they possess. They have been used in plant breeding to develop high yielding varieties; varieties with improved resistance to biotic and abiotic stresses, and enhanced nutritional content. Securing their conservation in the long-term is critical to enable the continuous development of crops’ varieties able to respond to future challenges. The work presented in this thesis is a contribution to the effort of understanding the ex situ conservation gaps of crop wild relatives, their expected response to climate change and their needs for conservation. Methods used in this thesis include species distribution modelling, gap analyses, a case study assessing the preliminary IUCN Red List categories, species distribution projections onto future climate change scenarios, and an estimation of the global value of crop wild relatives based on their likelihood of being used in plant breeding, and the contributions of their associated crops to human diets and agricultural production systems. The methods used here can be applied to more crop genepools for global conservation planning, and can also be adapted for analysis at the regional and national level. The results presented here are being used to improve the conservation of the wild relatives of 29 crops.

Climate change and anthropogenic activities threaten our global food security. One area of research that may help combat a future food crisis is the utilization of the genetic diversity available in wild plants. Crop wild relatives (CWR) are one such resource. They are the wild taxa most closely related to crops and from which diverse traits could be transferred to the crop. This project uses Norway as an example, to contribute towards methodologies to identify those CWR populations that are most important for conservation and use. This involves the creation of a priority list of CWR for Norway, in situ and ex situ diversity analysis of CWR populations, gap analysis and ecogeographic land characterization methodologies, predictive climate change analysis for CWR distributions and genetic diversity studies of taxa using Amplified Fragment Length Polymorphisms (AFLPs). Comprehensive in situ and ex situ national recommendations for the conservation of CWR in Norway are detailed. These include the incorporation of management plans for CWR populations within the Færder national park in Norway, the first instance of such conservation activities in Scandinavia. The scientific methods used and developed will help Norway meet its international obligations for conservation and use of genetic diversity of CWR and will contribute to the regional and global efforts to systematically conserve and utilize the diversity found in CWR.