The number phytopathogenic micromycetes is determined in the seeds of such cultivated varieties of cultural plant as soybeans, sunflowers, yellow mustard, buckwheat and thistle, which are grown by organic technology. It is shown that the number of micromycetes in the plant seeds differs significantly and ranges from 0.2 to 1.3 thousand NCO/g seeds. It depends on properties plants variety and hybrid, which are characterized by some certain set of physiological and biochemical characteristics that influences the formation seed mycobiome and it is quantitative composition. In the seeds varieties of these crops we identified such species of the phytopathogenic fungi as Alternaria alternate Fr., Fusarium oxysporum Schleht, Cladosporium herbarum Lket Gray, Botrytiscinerea Pers. Ex Fr., Ascochyta fagopyri Bres., Alternaria tenuissima (Kunze) Wiltshire, Aspergillus P. Micheliex Haller, Pénicillium Link. It was found that the species composition of phytopathogenic micromycetes in the seeds of soybean cultivar Kent and thistle Riches is much more diverse than the seeds other crops dominated by fungi A. alternate and F. oxysporum, which are characterized by different frequency of occurrence. These phytopathogenic fungi can cause plant diseases at different stages of ontogenesis, produce mycotoxins and reduce the quality of plant products. In the mycobiome of seeds buckwheat varieties Sophia, Sуn and sunflower hybrids Oscar and Oliver are dominated by fungi of the genus Pénicillium аnd Aspergillus (60–90%). The seeds affected by saprotrophic fungi can be reinfected during storage. This reduces its field and laboratory germination of the seeds. Saprotrophic fungi that dominate the seeds significantly impair its quality during storage and cause dangerous plant diseases in agrophytocenoses during the cultivation of this variety/hybrid. This requires the application of additional preventive protection measures of plants. Mycobioma mustard seeds of а yellow variety Ford represents a small number the phytopathogenic micromycetes. This may indicate its environmental safety in organic production. Thus, the analyzed research results indicate a significant differentiation in varieties species as to composition and number of phytopathogenic species of micromycetes in the seed mycobioma. Therefore, in order to avoid ecologic risks and biological contamination of agrocenoses, it is necessary to test the seeds, as on the density of the mycobiome and on the frequency of phytopathogenic micromycetes damage.

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