High-Throughput Sequencing Study of the Mycobiota of Barley Grain Collected in Northern and Central Italy and Accumulation of Fungal Secondary Metabolites

Barley grain provides an ecological niche in which fungal microorganisms can develop. The presence of mycotoxigenic genera can result in the accumulation of fungal secondary metabolites. The present study aims to survey barley grain samples collected from Northern and Central Italy by assessing: (1) the presence of fungal microorganisms using high-throughput sequencing of the internal transcribed spacer region; (2) the presence and quantification, by real-time quantitative PCR (RT-qPCR), of the main Fusarium species associated with Fusarium head blight; and (3) the presence and quantification of secondary metabolites produced by Fusarium and Alternaria using liquid chromatography–tandem mass spectrometry. Both potentially pathogenic genera (mainly within the Ascomycota division) and non-pathogenic genera (within both Ascomycota and Basidiomycota divisions) were detected. Alternaria and Cryptococcus were the dominant genera within Ascomycota and Basidiomycota divisions, respectively, in both macro-areas. Some genera, such as Aureobasidium and Cryptococcus, showed interesting negative correlations with several pathogenic genera. Two important mycotoxigenic genera (Alternaria and Fusarium) were detected, with RT-qPCR that revealed the predominance of Fusarium graminearum in the Northern macro-area. Fusarium secondary metabolites exhibited generally higher accumulation in the North, whereas Alternaria secondary metabolites were more evenly distributed across Italy, reflecting the abundance of the two genera. The co-occurrence of Fusarium and Alternaria secondary metabolites within single barley grain samples was also observed.