Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers

Abstract

The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly, Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deinococcus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum.

Keywords: Deinococcus-Thermus; group-specific primers; molecular diversity.

Figure 1

Location map of the study sites (triangles). For the hot springs, the water temperature is indicated in brackets. Genera belonging to the Deinococcus-Thermus phylum retrieved in each site are also indicated.

Figure 2

Neighbor-Joining tree based on 16S rRNA sequences recovered from Tataouine (labelled with the prefix DTat) and from hot springs 5, 7, 9, 10 and 11 (labelled with the prefixes Dtun-S5, Dtun-S7, Dtun-S9, Dtun-S10 and Dtun-S11, respectively). The tree is simplified to include one sequence per OTU and per collection site, as well as the most similar sequences from public databases. The number of sequences within each OTU is indicated at the leaves (n = x). A complete tree is shown in Figure S2.