High yield losses of crops due to plant pathogens represent a serious problem in agriculture. More effective and sustainable control measures, such as biological control, are essential. Most terrestrial plants, including important crop plants, benefit from a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi through enhanced nutrition and improved immune responses. Although this latter phenomenon, known as Mycorrhiza Induced Resistance (MIR), is well-reported and molecular responses to AM symbiosis have been observed, how AM fungi prime disease resistance is still poorly understood. Several factors and mechanisms have been suggested to impact the outcome of MIR, but how this phenomenon occurs and how different factors impact MIR is not known. Evidence suggests that AM fungal species differ in their abilities to defend plants and that plant species, and even varieties, can have differing colonisation levels leading to changing outcomes of MIR. However, the underlying molecular mechanisms on a biochemical level leading to alterations of MIR are not well understood and require examination of patterns related to MIR effects and involved molecular factors in these interactions to exploit the biocontrol potential of AM fungi. To achieve this, my doctoral thesis investigates some of these fundamental MIR knowledge gaps by combining interdisciplinary research including phenotyping observations as well as molecular approaches (transcriptomics and metabolomics). The results of my PhD research provide increased and novel insights into comprehensive phenotypic, transcriptional and biochemical patterns and mechanisms related to mediation of MIR. Investigation of basic plant gene expression patterns revealed the involvement of beneficial and pathogenic microbes in non-defence-related biological processes and shows that MIR is involved in a large number of processes within the transcriptomic profile. This thesis provided further evidence of the importance of AM fungal identity on the outcome of MIR and showed that the differences in metabolic profiles reflect these observations. My thesis also highlights the importance of studying MIR in natural contexts, where plants interact with diverse fungal communities, by showing the non-additive effects of AM fungal communities compared to single species observations. I also show that plant varieties with different potentials for AM fungal colonisation demonstrate opposing MIR metabolomic responses. Moreover, the potential involvement of down-regulated metabolic pathways to protect plants against pathogen addition has been demonstrated. These studies highlight the need for further investigations of the biochemical networks leading to the strength of MIR
