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Background: Understanding the dynamics of fungal communities in composting and vermicomposting systems is essential for optimizing waste management practices and minimizing pathogen risks. For this reason, this study assessed the fungal community structure and potential pathogenic risks in composting, vermicomposting and leachate systems amended with rabbit manure, using Illumina’s MiSeq platform for internal transcribed spacer (ITS) sequencing and FUNGuild analysis.
Results: Phylotypes from Basidiomycota were predominant in all treatments, while the pathogenic genus Microascus, initially abundant (37%), showed a significant reduction to 5% and 7% following composting and vermicomposting, respectively, and to 1% and 13% in their leachates. Given Microascus’s association with human skin diseases, proper handling of organic waste is critical before its agricultural use. In contrast, the FUNGuild analysis revealed a high abundance of saprotrophic fungi such as Aspergillus, Preussia, Botryotrichum, and Acremonium known for producing enzymes that promote nutrient cycling and soil fertility.
Conclusions: These findings highlight the potential for vermicomposting to reduce pathogen risks while enhancing fungal-driven nutrient recycling, offering practical insights for sustainable agriculture and organic waste management.
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