Novel biocontrol fungi for sustainable strawberry production

The modern diet determines the sharp increase in the production of berries in Europe. The cultivation of soft fruits has become particularly attractive for small farms in Slovenia and for rural development strategies, as it allows specialisation in products with high added value - vitamins, antioxidants and fibre. Botrytis species, especially B. cinerea, ranked as the second most important fungal plant pathogen, cause grey mould rot on more than 500 crops. Soft fruits such as strawberries are particularly susceptible to mechanical damage and to pre- and postharvest rot caused by fungi. The primary means of controlling Botrytis spp. is through the use of fungicides during the growing season; however, several Botrytis species have developed multiple resistances to fungicides, resulting in limited or ineffective chemical control. The long-lasting and hazardous effects of pesticides on the environment and human health have been of public concern for decades. Alternative plant protection strategies that replace pesticides in agriculture are urgently needed, and their development is part of national and European strategies for more sustainable and organic food production. One of the most promising approaches is the use of microbial antagonists. However, due to their limited efficacy, the search for more effective strains is needed. In addition, there is very little data on the mechanisms of biocontrol agents, and it would be of great importance to uncover the mode of action. Based on the reduced efficacy of chemical fungicides against B. cinerea, the increased demands for more sustainable/organic agriculture, we designed a research workflow to find more efficient antagonistic fungi capable of suppressing primarily the identified Botrytis species while negatively impacting the two other economically most important fungal diseases of strawberry, namely powdery mildew caused by Podopshaera aphanis and anthracnose caused by Colletotrichum acutatum. Among other, the research will uncover a novel principle of interaction of not-yet-commercialised fungal strains that suppress Botrytis spp. through soluble secondary metabolites. A broad spectrum of phylogenetically diverse fungal candidates present in our culture collections will be screened for relevant traits against Botrytis in vitro and in vivo assays. The most effective biocontrol strains will also be tested against P. aphanis and C. acutatum. The mode of interaction of the fungal antagonists with Botrytis will be described by transcriptomic and metabolomic analyses. Thus, soluble and volatile organic compounds associated with antagonism or genes expressed during the interaction will be identified. The efficacy of a fungal antagonist to protect strawberries in the laboratory often differs from its efficacy under real growing conditions. Therefore, we will conduct an in planta trial using a fungal antagonist to protect strawberries against Botrytis spp. as well as P. aphanis and C. acutatum. Its efficacy will be evaluated by high-throughput hyperspectral imaging, which will reveal the health status of plants based on changes in physiology in conjunction with chemometric analysis of leaves and quality of fruit produced. The results of this project will identify new fungal strains that are antagonistic to Botrytis spp. and can as well suppress powdery mildew and anthracnosis of strawberries. Importantly, the fungal interaction will be uncovered by transcriptional responses on the fruit, which is novel from a scientific perspective. In addition, an important advance will be made in evaluating plant health following the application of a biotic agent through high-throughput hyperspectral imaging and the development of predictive models for strawberry quality. Overall, the obtained data will enable the discovery of plant beneficial fungal traits and principles that could lead to commercialization and sustainable application in a pesticide reduced/free production of strawberries.