Molecular identification of actinomycetes in the button mushroom compost using analysis of 16S rRNA gene restriction fragment patterns

Thermophilic actinomycetes due to their ability to decompose the cellulolytic materials are of the main components of compost micro-flora of the button mushroom. Different methods including morphological, biochemical and molecular techniques have been used to separate the actinomycetes into different groups. PCR-based methods such as the pattern of amplified rDNA restriction analysis (ARDRA) have been shown to be useful in differentiating between bacterial species within a genus. Comparison of restricted fragments patterns from isolated bacteria with a database containing 16S rRNA gene sequences of all validly published filamentous from GenBank using In silico digestions is a rapid method for identification of actinomycetes. Thermophilic actinomycetes of compost were isolated on culture medium using dilution methods and incubation at 46°C. The 16S rRNA gene of each isolates were amplified by PCR and digested by restriction endonucleases. The restricted pattern for each enzyme was determined by electrophoresis. Unknown isolates were identified using amplified rDNA restriction analysis. Most isolated actinomycetes from the white button mushroom compost belonged to Streptomyces genus which has a significant role in degradation of plant residuals and compost production.