So as to provide new insight into the diversity of Archaea in dry mud, sediment and water from Lake Elmenteita in Kenya, an investigation using a culture-independent approach was conducted after extraction of total genomic DNA from the environmental samples using suitable extraction methods. Small insert clone libraries were constructed by amplifying 16S rRNA genes using archaea-specific primers, followed by cloning from which 94 non-chimeric sequences were obtained and a total of 34 operational taxonomic units (OTUs) were identified. The OTUs were grouped into Thaumarchaeota (6%) and Euryarchaeota (94%). Approximately 90% of the clones were related with genes from uncultured Archaea, compared to the 10% that showed affiliation with genes from previously cultured Archaea. The similarity of the sequenced clones to type strains was consistently lower than the similarity to uncultured members of Archaea. Clones from water and sediment were dominated by sequences from Euryarchaea, while clones from the dry mud samples showed affiliations to both Euryarchaeota and Thaumarchaeota, with the predominant phylum being Euryarchaeota. This is the first study reporting the presence of representatives of Thaumarachaeota from Lake Elmenteita and adds sequences from Lake Elmenteita to the developing database of 16S rRNA clone libraries obtained from environmental sources.
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