Microorganisms have important roles in the composting process for the production of the commercial button mushroom, Agaricus bisporus. A culture-independent survey of microbes within mushroom substrate was conducted for compost collected after pasteurization during Phase II. An efficient method for DNA extraction from compost was developed. PCR was employed to characterize fungal and bacterial members using sequences of the small subunit ribosomal DNA. Of the 110 fragments sequenced, 37 were bacterial sequences corresponding to at least 35 different strains representing seven bacterial divisions. Most sequences identified were not present in existing databases, suggesting compost may contain many novel bacteria. Seventy-three fragments were fungal sequences, corresponding to at least 26 unique strains affiliated with 4 species. The complexity of the fungal community within Phase II mushroom compost appeared much lower. Most fungal rDNA fragments were identical to the sequence of the thermophile Scytalidium thermophilum.; Fungal diversity in Phase I and Phase II composts produced by aerated bunker and conventional windrow Phase I systems was examined. The selected primers amplified plant rDNA, and a range of 18S rDNA related to ascomycetes, zygomycetes, stramenopiles, protozoa, and dinoflagellates. Sixty-nine different phylotypes and 183 redundant sequences were identified. Most redundancies (135) were phylogenetically affiliated with Scytalidium thermophilum . The most notable difference between the two Phase I methods concerned the profile of samples at the end of Phase I (filling). At this stage, traditional compost harbored more diverse phylotypes, however both technologies produced a substrate with similar communities at the end of Phase II.; An investigation of fungal strains within the S. thermophilum species complex was conducted. Gene phylogenies inferred from partial β-tubulin and internally transcribed spacer (ITS) regions of the rDNA were highly concordant, providing evidence recognizing the distinction of three groups within the S. thermophilum complex, with morphological characterization supporting such partitions. Sequence analyses indicate that S. thermophilum and the type species of Humicola are closely related and belong within the order Soradriales, precluding any previous relationship with Scytalidium at the generic level.
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