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Background: Champignon mushroom production is strongly influenced by the occurrence of pathogenic bacteria and fungi causing different kinds of diseases which can significantly lower the yield. Green mold disease is one of the most aggressive diseases of champignon mushrooms. In champignon production, green mold disease is connected to fungal species belonging to genus Trichoderma. The most aggressive are T. aggressivum f. europaeum (mainly present in Europe) and T. aggressivum f. aggressivum (mainly present in North America), but also T. harzianum. Objectives: In this research we aimed to explore the efficiency of DNA metabarcoding approach to detect Trichoderma species present in compost and casing soil during champignon cultivation. Methods: Genomic DNA extracted from compost and casing soil was used as a template for amplification and sequencing of an ITS2 fragment. High-throughput sequencing was performed on the Illumina NovaSeq 6000 platform. Raw sequence data was processed using next-generation microbiome bioinformatics platform QIIME2. In total, 332 operational taxonomic units were defined and the trend of succession in fungal communities of compost and casing soil were detected between different time dependent sample series. Results: We identified eight Trichoderma species among which T. harzianum and T. aggressivum. The first was detected in all sample series, while the second was detected only in casing soil samples. Using DNA metabarcoding it was possible to detect aggressive Trichoderma species even before the appearance of visible green mold. However, there was no clear pattern in Trichoderma spp. detection among time dependent sample series. |
