Molecular methods in quantification and community analysis of Fusarium fungi to evaluate a risk of mycotoxin contamination in cereals

Fusarium head blight (FHB) is an economically important cereal infecting plant disease that is caused mainly by fungal species belonging to genus Fusarium. Some of the Fusarium species pro-duce mycotoxins that cause a food safety concern for both humans and animals. Especially im-portant mycotoxin producing fungi causing FHB is Fusarium graminearum but often Fusarium species form a disease complex where different Fusarium species co-occur in the infected cereals. Effective management strategies for FHB are needed and development of these management methods requires information about the composition and abundance of the whole Fusarium community. Molecular quantification methods for detecting individual Fusarium species and subgroups exist but method for detection and quantification of all species belonging to Fusarium sp. is still lacking. In this study a new TaqMan based qPCR method targeting the Fusarium -specific elongation factor region (EF1a) (FusE) was developed for detection and quantification of Fusarium sp. The FusE method was proven as sensitive method with detection limit of 1 pg of Fusarium DNA and mean efficiency of 95 %. Fusarium abundance results from cereal samples correlated significantly with deoxyvalenol (DON) toxin levels in all years when samples were taken. In addition, with new metabarcoding method, the whole Fusarium community in Finnish oat samples was characterized. A shift from F. culmorum to F. graminearum in FHB infected cereal grains have been detected in Europe and results of this study confirms that. These new molecular methods can be used in estimation of mycotoxin risk in cereals and knowledge gained from using these methods can be applied in developing and selecting effective management strategies for FHB.