Genotyping of uncultured archaea in a polluted site of Suez Gulf, Egypt, based on 16S rRNA gene analyses

Culture-independent 16S rRNA gene analysis approach was used to explore and evaluate archaea in a polluted site, El-Zeitia, Suez Gulf, Egypt. Metagenomic DNA was extracted from a sediment sample. Archaeal 16S rRNA gene was PCR amplified using universal archaeal primers, followed by cloning and direct analyses by sequencing. Rarefaction analysis showed saturation, recording 21 archaeal 16S rRNA gene phylotypes, which represented the total composition of archaea in the studied sample. Phylogenetic analysis showed that all recorded phylotypes belonged to two archaeal phyla. Sixteen phylotypes were located in the branch of methanogenic Euryarchaeota and more closely related to species of the genera Methanosaeta and Methanomassiliicoccus. Five phylotypes were affiliated to the new archaeal phylum Thaumarchaeota, which represented by species Candidatus nitrosopumilus. The recorded phylotypes had unique sequences, characterizing them as new phylogenetic lineages. This work is the first investigation of uncultured archaea in the Suez Gulf, and implicated that the environmental characteristics shaped the diversity of archaeal 16S rRNA genes in the studied sample.