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Fungal pathogens are an international concern regarding their impact on numerous crops with diseases such as the Fusarium wilt, grey molds, blue molds or downy mildews that cause colossal yield losses both at pre- and post-harvest stages all over the world. The fungal diseases are usually associated with the infection and accumulation of mycotoxins in plant products and derivate foods. Alternative approaches of biological control that are non-chemical and eco-friendly have been studied such as the crop rotations or the application of organic phyto-protective amendments using living organisms. Many different bacterial families have been identified but accounting for low abundance in the total communities. The participation of the predominant families in 3-day-old soil decreased after 28 days of incubation. The fungal community of the reference soil was more diversified as compared to the fungal communities of the amendments.