Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes

PLoS One. 2013 Aug 30;8(8):e72577. doi: 10.1371/journal.pone.0072577. eCollection 2013.


Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most "extreme" lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and 'nitrifier denitrification' were also confirmed by mRNA transcript analyses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Base Sequence
  • Biodiversity*
  • Databases, Genetic
  • Ethiopia
  • Eukaryota / growth & development*
  • Gene Expression Regulation
  • Lakes / microbiology*
  • Phylogeography*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Ribosomal / genetics


  • RNA, Messenger
  • RNA, Ribosomal

Grant support

This work was supported by the Norwegian Research Council (project no. 179560), L. Meltzers høyskolefond (project no. 805372) and the Norwegian Agency for Development Cooperation (NUFU project no. 802779: “Biotechnology and Diversity of Ethiopian Soda Lakes”). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.