Characterization of mycobiota in faba beans infected with Alternaria spp.

Leaf diseases pose a serious threat to faba bean production. Leaf blotch of faba bean, caused by Alternaria spp., has become increasingly widespread and destructive in several countries. The infection of plants by pathogens can be influenced by various factors associated with the host plant, environmental conditions, and the presence of other microorganisms. The phyllosphere and endosphere play a critical role in plant health and disease development. This study aimed to evaluate the factors shaping the structure and diversity of fungal communities associated with faba beans infected by Alternaria spp. Plant samples were collected in 2024 from two intensively managed faba bean production fields in the central region of Latvia. Fungal assemblages were characterized using an ITS region metabarcoding approach via Illumina MiSeq sequencing. Among the assigned amplicon sequence variants (AVS), 65% belonged to the phylum Ascomycota, while approximately 4% were classified as Basidiomycota. Alternaria and Cladosporium were the dominant genera across samples. The alpha and beta diversities of fungal communities were higher during the flowering of faba beans compared with ripening. A higher abundance of Basidiomycota yeasts was observed during flowering; in contrast, the Cladosporium genus was significantly more abundant during ripening. Alternaria DNA was detected in all plant tissues, including leaves that exhibited no disease symptoms. The diversity and composition of fungal communities were significantly influenced by sampling time and the presence of leaf blotch, caused by Alternaria spp.