Quantification of Endospore-Forming <i>Firmicutes</i> by Quantitative PCR with the Functional Gene <i>spo0A</i>

Bacterial endospores are highly specialized cellular forms that allow endospore-forming <i>Firmicutes</i> (EFF) to tolerate harsh environmental conditions. EFF are considered ubiquitous in natural environments, in particular, those subjected to stress conditions. In addition to natural habitats, EFF are often the cause of contamination problems in anthropogenic environments, such as industrial production plants or hospitals. It is therefore desirable to assess their prevalence in environmental and industrial fields. To this end, a high-sensitivity detection method is still needed. The aim of this study was to develop and evaluate an approach based on quantitative PCR (qPCR). For this, the suitability of functional genes specific for and common to all EFF were evaluated. Seven genes were considered, but only <i>spo0A</i> was retained to identify conserved regions for qPCR primer design. An approach based on multivariate analysis was developed for primer design. Two primer sets were obtained and evaluated with 16 pure cultures, including representatives of the genera <i>Bacillus</i>, <i>Paenibacillus</i>, <i>Brevibacillus</i>, <i>Geobacillus</i>, <i>Alicyclobacillus</i>, <i>Sulfobacillus</i>, <i>Clostridium</i>, and <i>Desulfotomaculum</i>, as well as with environmental samples. The primer sets developed gave a reliable quantification when tested on laboratory strains, with the exception of <i>Sulfobacillus</i> and <i>Desulfotomaculum</i>. A test using sediment samples with a diverse EFF community also gave a reliable quantification compared to 16S rRNA gene pyrosequencing. A detection limit of about 10⁴ cells (or spores) per gram of initial material was calculated, indicating this method has a promising potential for the detection of EFF over a wide range of applications.