Characterization of Fungi Communities in Organic Soybean Seeds Using DNA Sequencing: Effects of Cultivar and Location

Organic soybean seeds are susceptible to colonization by numerous fungal pathogens, which can reduce their germination capacity and nutritional quality. This study evaluated fungi transmitted by seeds and their effects on selected seed quality parameters, as well as the influence of variety, location and growing season. In total, 471 fungal isolates belonging to 24 genera and 37 species were obtained from three soybean varieties (Erica, Es Commandor and Cerez PZO) cultivated at two locations during the 2022-2023 seasons. All obtained isolates were identified based on <i>ITS</i> sequencing, and <i>Fusarium</i> isolates were further characterized to the species level using <i>TEF</i> and <i>RPB2</i> markers. <i>Fusarium</i> spp. was the most frequently isolated genus, accounting for 35.7% of all isolates, followed by <i>Alternaria</i> spp. (15.9%) and <i>Aspergillus</i> spp. (11.9%). Fungal frequency and species diversity differed significantly between years. Seed germination capacity was significantly lower in 2023 than in 2022 and coincided with higher fungal colonization, lower spring temperatures, and increased rainfall. A significant negative Pearson's correlation (r = -0.58, <i>p</i> < 0.05) was found between fungi abundance and seed oil content, indicating a direct impact of fungal colonization on nutritional quality. These results highlight the role of environmental conditions in seed-borne pathogen communities and the need for monitoring and seed health management to ensure soybean seed quality.