Development of Real-Time PCR Primer and Probe Sets for Detecting Degenerated and Non-degenerated Forms of the Butanol-Producing Bacterium Clostridium acetobutylicum ATCC 824

Degeneration is one of the limiting factors in butanol fermentation, and it must be monitored and prevented for stable butanol production. In Clostridium acetobutylicum ATCC 824, the most well-known butanol-producing microorganism, degeneration is caused by the loss of the pSOL1 plasmid that carries essential genes involved in solvent production. In this study, we designed two specific primer and probe sets for real-time qPCR (RT-qPCR) detection of C. acetobutylicum ATCC 824 (the C. aceto set) and pSOL1-possessing C. acetobutylicum ATCC 824 (the DGS set). Specific primer and probe sets were designed on the basis of the 16S rDNA sequence and pSOL1 sequence. The number of degenerated C. acetobutylicum could be quantified by subtracting the number of C. acetobutylicum ATCC 824 containing pSOL1 from the total number of C. acetobutylicum ATCC 824. The primer and probe sets permitted the specific detection and quantification of degenerated C. acetobutylicum and total butanol-producing C. acetobutylicum by RT-qPCR.