Microbiota associated with oyster mushroom substrates using culture dependent and targeted-metagenomics methods / Ameertha Ponnusamy

Ameertha , Ponnusamy (2022) Microbiota associated with oyster mushroom substrates using culture dependent and targeted-metagenomics methods / Ameertha Ponnusamy. Masters thesis, Universiti Malaya.

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Abstract

The globally mushroom cultivation industry is challenged with frequent green mold contamination that is often thought to be caused by the green mold - Trichoderma spp. However, the farmers and researchers do not have much insight on the possible factors that lead to the frequent but random green mold contamination in the mushroom cultivation industry. Therefore, this study aims to investigate the possible role of the natural microbiota present in the mushroom substrate has on green mold contamination. To do so, both culture-dependent and culture independent (16 srRNA targeted- metagenomic) approaches were used in this study to identify and compare the diversity of microbiota found in both healthy and contaminated mushroom substrates collected from a local mushroom farm at different stages of harvest. The study found that the green mold contaminated mushroom substrates had the highest total heterophilic bacteria count, 9.5×10⁷cfu/g. In general, the total heterophilic bacteria count in mushroom substrates increased from after sterilization stage (<10cfu/g) to reach the maximum count in contaminated stage (9.5×10⁷cfu/g) of harvest. The findings revealed that bacterial community from the Proteobacteria phylum was the most abundant in both final harvest (healthy) and green mold contaminated substrates. However, there was a shift in the bacterial diversity in the cultured bacterial populations with the increase of Gammaproteobacteria and the decrease of Bacilli after sterilisation of substrate along the cultivation stages. Gammaproteobacteria, the highest occurring class of bacteria in contaminated substrate with Enterobacteriaceae being the largest community indicates possible unhygienic practices during cultivation process. High abundance of Pseudomonas, Enterobacter and Stenotrophomonas in contaminated substrate from the cultured population and metagenomic data may also be contributing to Trichoderma colonisation.

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