Developing a Novel Approach of rpoB Gene as a Powerful Biomarker for the Environmental Microbial Diversity

Use of the rpoB gene (the encoding the β-subunit of RNA Polymerase gene), a potential alternative biomarker to the 16S rRNA gene, has been limited to environmental microbial investigation for a long time because of the lack of effective primers. Here we developed a novel rpoB gene-based approach using a newly designed primer pair and tested it in three different environmental water samples with the traditional library method. The results showed that our novel approach presented different microbial diversity patterns from the different environmental samples. Compared to previous rpoB gene based reports, the first retrieved groups in our approach included mainly α-Proteobacteria, δ-Proteobacteria, Planctomycetes, Verrucomicrobia, Firmicutes, Chlorofexi and Actinobacteria, which greatly expanded the potential ability of the rpoB gene approach for environmental surveys. Most importantly, the use of the traditional clone library approach with the novel rpoB gene primers greatly supplement the microbial diversity based on the 16S rRNA gene approach with the universal primer pair (27f and 1492r), at all phylum, class, order, family and genus levels, indicating a powerful complementary method and a potential alternative biomarker of the current popular NGS (next-generation sequences) technologies for the environmental microbial investigation.