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Research article - Peer-reviewed, 2022

Prokaryotic and eukaryotic microbial diversity from three soda lakes in the East African Rift Valley determined by amplicon sequencing

Jeilu, Oliyad; Gessesse, Amare; Simachew, Addis; Johansson, Eva; Alexandersson, Erik


Soda lakes are unique poly-extreme environments with high alkalinity and salinity that support diverse microbial communities despite their extreme nature. In this study, prokaryotic and eukaryotic microbial diversity in samples of the three soda lakes, Lake Abijata, Lake Chitu and Lake Shala in the East African Rift Valley, were determined using amplicon sequencing. Culture-independent analysis showed higher diversity of prokaryotic and eukaryotic microbial communities in all three soda lakes than previously reported. A total of 3,603 prokaryotic and 898 eukaryotic operational taxonomic units (OTUs) were found through culture-independent amplicon sequencing, whereas only 134 bacterial OTUs, which correspond to 3%, were obtained by enrichment cultures. This shows that only a fraction of the microorganisms from these habitats can be cultured under laboratory conditions. Of the three soda lakes, samples from Lake Chitu showed the highest prokaryotic diversity, while samples from Lake Shala showed the lowest diversity. Pseudomonadota (Halomonas), Bacillota (Bacillus, Clostridia), Bacteroidota (Bacteroides), Euryarchaeota (Thermoplasmata, Thermococci, Methanomicrobia, Halobacter), and Nanoarchaeota (Woesearchaeia) were the most common prokaryotic microbes in the three soda lakes. A high diversity of eukaryotic organisms were identified, primarily represented by Ascomycota and Basidiomycota. Compared to the other two lakes, a higher number of eukaryotic OTUs were found in Lake Abijata. The present study showed that these unique habitats harbour diverse microbial genetic resources with possible use in biotechnological applications, which should be further investigated by functional metagenomics.


microbial diversity; extremophiles; haloalkalophiles; operational taxonomic units; soda lakes

Published in

Frontiers in Microbiology
2022, volume: 13, article number: 999876

Authors' information

Jeilu, Oliyad (Oumer, Oliyad Jeilu)
Addis Ababa University
Swedish University of Agricultural Sciences, Department of Plant Breeding
Gessesse, Amare
Addis Ababa University
Simachew, Addis
Addis Ababa University
Swedish University of Agricultural Sciences, Department of Plant Breeding
Swedish University of Agricultural Sciences, Department of Plant Protection Biology

UKÄ Subject classification

Other Environmental Biotechnology

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