Type II chaperonin gene as a complementary barcode for 16S rRNA gene in study of Archaea diversity of petroleum reservoirs

Abstract

Archaea is an important component of the microbial community in subsurface petroleum reservoirs. Here, we compare Type II chaperonin (thermosome) and 16S rRNA gene as phylogenetic markers for revealing archaea in petroleum reservoirs. Evaluation of barcode gap of 16S rRNA targets and thermosome targets within 221 Archaea genomes available showed that thermosome targets have a much larger barcode gap than 16S rRNA, indicating that thermosome would provide improved species resolution over the 16S rRNA target. We then applied this combined approaches to two samples obtained from deep subsurface petroleum reservoirs. In general, members affiliated with the family Archaeoglobaceae were abundant in both samples regardless of the method used. While methanogenic archaea (Methanobacteriaceae, Methanosarcinaceae, Methanocalculaceae) were detected predominantly by 16S rRNA sequencing, thermosome sequences, however, showed the presence of archaeal members within the unclassified Thermofilaceae and unclassified Desulfurococcales, suggesting significant discrepancies between the two approaches to our understanding of the archaeal community taxa in deep subsurface petroleum reservoirs. Given these, Type II chaperonin (thermosome) can be a potential complementary biomarker in addition to 16S rRNA gene analysis of microbial community composition and diversity for more detailed information.