Composting involves complex microbial processes in which intricate metabolic activities drive the biological decomposition of organic substrates. As is typical of solid state fermentation, this composting environment is characterized by low moisture content and thermophilic transitions that allow for the characterization and identification of new enzymes, bio-control agents and secondary metabolites. In this study, switch grass(shelter) was supplemented with dog food to provide a C: N ratio of 15 and composted using forced aeration at various moisture contents in highly-instrumented reactors . A protocol for the rapid co-extraction of DNA and RNA from compost samples was developed and small sub-unit-based rRNA probes were used to quantify the relative abundance of various phylogenetic groups of fungi, bacteria, Bacillus, lactic acid bacteria and actinomycetes. Two major shifts in the microbial populations were observed – one between 12 and 24 hours and the other between 55 and 65 hours. These changes in community structure coincided with rising temperatures and drops in pH, resulting in a prevalence of bacteria and lactic acid bacteria in the first 60 hours, followed by a dominance of fungi, Bacillus and actinomycetes in the later stages of composting.