During wheat colonisation, toxigenic Fusarium species produce substantial numbers of mycotoxins, which pose serious adverse health effects in human and animals. The current control strategies rely on the use of resistant varieties and synthetic fungicides. However, these control measures are not always effective. Moreover, excessive use of fungicides has led to the development of resistance in many toxigenic Fusarium species. Therefore, there is an urgent need to develop an effective and sustainable method to minimise wheat mycotoxin content. The goal of this project is to provide novel insights into the role of wheat microbiome in preventing mycotoxin contamination and to identify wheat varieties and microbes with potential to promote the suppression of mycotoxin production in wheat. Fungicide untreated winter wheat varieties will be collected from three different experimental field sites in Ireland and Northern Ireland. Then, a targeted metabolomics approach will be used to quantify 10 important mycotoxins in winter wheat samples, to identify resistant and susceptible varieties. Subsequently, DNA will be extracted from the samples and a culture-independent shotgun metagenomic high-throughput sequencing will be applied to characterise the microbiome diversity and function of wheat varieties. Robust statistical tests and bioinformatics tools will be used to analyse and compare sequences and mycotoxin level data, to identify specific microbial species and metabolic pathways that are significantly correlated with wheat varieties found resistant and susceptible to mycotoxin accumulation. Ultimately, the identification of specific wheat varieties that recruit microbiomes that can inhibit mycotoxin production opens new horizons for breeding next-generation crops depending less on fungicide input and resistant to mycotoxin contamination. This project and the planned training activities will further enhance my skills to become an independent researcher.

As the world population continues to grow and a shortage of protein supply is foreseen, there is a need to identify new and sustainable protein sources. While these alternative proteins must be of high nutritional quality, they also need to be safe for consumption. Dietary proteins and their digestion products can influence a number of regulatory systems, including the immune system. By interacting with elements of the immune system, proteins can help balance and stabilize immune responses, but may also trigger adverse effects such as allergic reactions. While the effects of proteins and peptides on the adaptive immunity have been examined in a number of studies, few have studied how these molecules are absorbed through the small intestine and interact with the innate immune system. Since, in order to trigger an immune response proteins must first be transported across the intestinal wall and interact with the innate immune system, understanding these processes is key to determining the immunological effects of protein consumption. The aim of the proposed project is to develop an in vitro model to evaluate the impact of dietary proteins on the immune system. This research will first examine the uptake of proteins and their digests across the intestinal wall using cellular models mimicking the intestinal epithelium and subsequently investigate the effect of the absorbed proteins/peptides on the immune system’s key players, including the dendritic and T cells. The model system that this research aims to develop could help shed light on the roles played by dietary proteins in regulating intestinal immunity and serve as a tool to evaluate the immunological properties of novel and sustainable proteins. Thus, this research is of relevance not only to the European food industry, but also to public health.

Neonectria ditissima is the causal agent of European fruit tree canker, one of the most devastating apple diseases in Europe. This pathogen causes cankers on apple twigs, branches and main stem, which may lead the loss of the whole tree. While chemical control is the essential component in the management of this disease, no suitable biocontrol products are commercially available against N. ditissima. Following the commitment of the European Union to prefer sustainable biological methods in integrated pest management strategies (Directive 2009/128/EC), BioNeedit will contribute in the development of a new biocontrol product to control European fruit tree canker disease. To achieve this objective, potential antagonistic microorganisms against N. ditissima will be selected i) based on the beneficial role of the microbiome found in N. ditissima infected and healthy tissues of apple trees, ii) through a systematic stepwise antagonist screening program, iii) testing the antagonist behaviour of the microorganisms against N. ditissima in a robust and cost-effective bioassay in planta and iv) evaluating the up-scaled biomass production of the selected antagonists. This multidisciplinary approach ensures that the selected microorganisms will not only have antagonistic properties, but will also fulfil the basic criteria regarding commercial production, safety and registration of plant protection products, as well as the ecological needs for the applications on the field. This approach will also overcome major constrains in the development of a biocontrol product and will reduce additional costs on its registration procedure. BioNeedit will mean a step forward in my career, broadening my existing Plant Pathology expertise and providing me new training in Biological Control. This project will expand my international network to a large group of active scientists and a biocontrol company that will help me to consolidate a position as a mature researcher in academia and/or industry

Poultry products are the most consumed source of animal protein globally. To enable current and future poultry genetic improvement towards climate adaptation and sustainable farming practices to meet future nutritional demands, it is essential to maintain and make available the existing genetic diversity within and between the breeds. Gene banks can assist in conserving genetic diversity and reintroduction and implementation of important traits or genetic variants into poultry lines. The main goal of CRYOCHICK is to develop effective cryopreservation methods for ex-situ conservation of male and female chicken germplasm. Existing strategies and methods for gene banking of chicken reproductive material are not adequate for several reasons such as poor fertility rate of cryopreserved semen, the contraceptive effect in hen of glycerol (the most effective sperm cryoprotectant), the current impossible cryopreservation of chicken oocytes due to its telolecithal structure, while semen alone does not capture genes of mitochondria and the W sex-chromosome. Therefore, new effective cryopreservation methods for both male and female chicken germplasms, as well as new strategies for maintaining and using the stored cryopreserved materials for cost-effective gene banking are required. The methods and strategies developed will likely also benefit other poultry species and conservation of wild relatives. CRYOCHICK comprises a high level training program for Dr. Bernal and different coordinated actions performed by prestigious institutes from different countries and research fields promoting international collaboration, interdisciplinarity and transfer of top knowledge to the private sector. The European competitiveness will be reinforced by addressing, with the highest level of knowledge, important global scientific and societal concerns such as maintenance of biodiversity and food security, both serious threatened by climate change.

Life, with all its diversity, is in crisis. As humans increasingly encroach on biologically complex semi- natural landscapes, no organism, place or ecological function remains unaffected. While all 196 parties (195 countries plus the European Union) to the UN Convention on Biodiversity (CBD) have agreed to monitor the state of biodiversity, the currently available methods to do so leave much to be desired. Traditional monitoring involves the field observation of species by trained specialists, aided by skilled volunteers, whose expertise is restricted to specific biotic groupings. In a process that is both time consuming and inconsistent across time and space, botanists identify and record the presence of plant species and ornithologists the bird biota, resulting in 'unpopular' biotic groups such as fungi, bacteria and insects being under-observed or escaping identification altogether. In this project, a fundamentally different approach to terrestrial biodiversity monitoring couples next generation satellite remote sensing with environmental DNA (eDNA) profiling, complemented where available by legacy human-observed datasets. Satellite remote sensing is able to survey the environment as a single, continuous, fine-resolution map, while eDNA profiling can rapidly quantify much greater taxonomical and functional breadth and depth than human field observation. This project combines, for the first time, these two powerful, cutting-edge techniques for monitoring biodiversity at the global level in a consistent manner. Following from this, another key innovation will be the deepening of our scientific understanding of how biodiversity is impacted by anthropogenic pressure as well as by natural environmental gradients. In concert, these scientific developments will enable the accurate and fine grain monitoring of biodiversity from space – a ground-breaking contribution to the quest to meet the UN Sustainable Development Goals and CBD Aichi targets.