Fungal diversity: From isolation and characterisation of populations to utilisation of fungal strains in plant disease control

The inconsistency of biocontrol agents (BCAs) applied to manage disease problems in field crops remains a major constraint to the development of novel BCAs. Many organisms from plants are adapted to their specific habitat, making it difficult for introduced BCAs to find a niche. We search for novel BCAs in habitats where they potentially interact with pathogens of interest, predicting that organisms isolated from environments where they are intended for use are more likely adapted to environmental conditions that favour development of specific diseases. Focusing on endophytic fungi may be advantageous since they colonise plants internally and are thereby potentially protected better from environmental stresses. In wheat and tomato plants, we combined cultivation dependent and independent approaches to obtain a deep understanding diversity and structure of endophytic mycobiomes, aiming at identification and isolation of novel reliable BCAs. Assessing the lifestyle of fungal endophytes originating from healthy tomato roots on tomato seedlings revealed the presence of both beneficial endophytes including Pseudeurotium sp. and four latent pathogen taxa. These tomato root pathogens were also the most dominating taxa based on community meta-barcoding. Intriguingly, Pseudeurotium species, not previously reported as beneficial to plants, were also highly abundant, indicating that this genus may hold novel potential BCAs. Taken together, complex interactions between members of the microbiome are suggested to maintain anequilibrium in the community, preventing pathogens from causing disease. In wheat spikes, endophyte communities were dominated by basidiomycete yeasts before anthesis while shifting towards a more opportunistic ascomycete-rich community during kernel development. These dynamics were interrupted when Fusarium spp. colonised wheat spikes and the pathogens excluded other fungi from floral tissues and reduced the community diversity. However, the presence of several endophytes correlated negatively with Fusarium spp. and linked with spikes staying healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium and the yeasts Itersonillia and Holtermanniella, suggesting they may represent an unexplored source of potential BCAs in wheat. Based on a community analysis of the wheat mycobiome from seed to plant to seed again in one growth season, it is evident that the structure of the endophytic microbiome is highly dependent on e. g. organ specific interactions between host genotype and abiotic climate condition. This emphasises the importance of searching for potential BCA in habitats matching both biotic and abiotic factors conducive to pathogen infection and disease development. Finally, the screening approach is in our opinion equally important to finding candidate strains. We firstly strive to evaluate their biocontrol potential in plant bioassays mimicking some natural environmental conditions. From our experience, in vitro inhibitory activities often do not correlate with in planta biocontrol efficacy. In fact, the best performing BCA strains against two important wheat diseases showed no growth inhibition of their causal organisms, Fusarium spp. and Zymoseptoria tritici, in dual cultures. This may reflect that mechanism of induced resistance cannot be discovered in the absence of the plant.