Estimation of distribution of a commensal thermophile in soil by competitive quantitative PCR and terminal restriction fragment length polymorphism analysis

Abstract

Symbiobacterium toebii has been previously reported as a novel commensal thermophile exhibiting a commensal interaction with thermophilic Geobacillus sp. SK-1. We investigated the distribution of this commensal thermophile in various soils using molecular methods, such as quantitative PCR and terminal restriction fragment polymorphism analysis. Based on a nested competitive quantitative PCR, the 16S rDNA of the commensal thermophile was only detected in compost soils at about 1.0×104 copies per gram of soil, corresponding to 0.25×104 cells per gram of soil. However, in an enrichment experiment at 60°C, about 1.0×108 copies of 16S rDNA molecules were detected per ml of enriched culture broth for all the soils, and more than 0.1 mM indole accumulated as the product of commensal bacterial growth. When incubated at 30°C, neither the 16S rDNA of the commensal bacterium nor any indole accumulation was detected. Accordingly, even though the 16S rDNA of the bacterium was only detected in the compost soils by a nested PCR, the presence of the 16S rDNA molecules of commensal thermophile and accumulation of indole in all the enriched cultures appeared to indicate that the commensal thermophile is widely distributed in various soils.