Metagenomic Exploration of Ethiopian Soda Lake Sediments: Microbial Diversity and Community Structure

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Addis Ababa Universty


It is estimated that less than 1% of all known environmental bacteria are culturable. It is currently believed that the uses of genetic approaches including metagenomics can bypass culturing of microorganisms and allow the identification of novel gene sequences and complete metabolic pathways of unculturable microorganisms directly from the environment. In this study, 16S- rRNA-based metagenomics was used to investigate the microbial community composition and phylogenetic relationships of Chitu, Shalla and Abijata soda lakes in the Ethiopian Rift Valley. Four 16S- rRNA-clone libraries were constructed for Chitu and Shalla lakes by using environmental DNA from sediment samples and 16S rRNA primers specific to bacterial and actinobacterial domains. In addition, 454-pyrosequencing was used to identify microbial phylogeny and compositions of Chitu, Shalla and Abijata soda lakes using the V3-V4 hypervariable specific regions of the bacterial 16S-rRNA genes with bar-coding strategy. Moreover, metagenomic approaches were used to construct a 40Kb fosmid (pCC1FOS vector) metagenomic DNA library of Chitu Soda Lake. Potential enzymes, metabolic genes and pathways were detected using functional and sequence- based metagenomic. 16S rRNA clone sequences of Chitu and Shalla Lakes were related to low and high G+C Gram-positive bacteria (Firmictes and Actinobacteria), CFB, and Protobacteria of the γ-, α-, ß- and Δ- Proteobacteria subdivisions. Most of the clones were phylogenetically allied with members of the γ- subdivision of Protobacteria (accounted for 34–43% of sequences), followed by Firmicutes (affiliated sequences at 16–26%). Both lakes were found to harbor biotechnologically and ecologically significant representatives of microbes that belong to the members of the group Rhodobaca, Alkalimonas, Nitrinicola, Thioalkalivibrio, Methylophaga, Desulfuromusa, Bacillus, Clostridium, Dethiobacter, Cytophagales, Actinobacteria, and Bacteroidetes. Barcode- tagged 454 pyrosequencing of prokaryotic community of Chitu, Shalla, and Abijata soda lakes revealed much wider diversity and novel representatives of microbial species that mostly included the methanogenic archaea (Methanocalculus), methane-oxidizing (Methylomicrobium sp.), Cyanobacteria, photosynthetic purple bacteria (Halorhodospira), non-sulfur purple bacterial genera (Rhodobaca), SOB (Thioalkalivibrio, Thioalkalispira, Sulfurimonas), SRB (Desulfobacterium, Desulfosarcina, Desulfurivibrio, Desulfonatronovibrio), Actonobacteria, Anoxybacillus, Bacillus, Clostridia, Nitrospira, Paracoccus, Rhodobacteraceae, Pseudomonas, Bacteroidetes, Deinococcus-Thermus, Planctomycetes, and Spirochetes. A total of 288 Mb metagenomic DNA Fosmid library size was constructed from Lake Chitu sediments in Ethiopian Rift Valley area. The plate screening of 7, 200 of total Fosmid clones of the lake sediments resulted significant proteolytic, amylolytic, cellulosic enzyme activities. Besides, sequence-based functional analysis of Lake Chitu Fosmid DNA using Hiseq 2000 (Illumina) provided novel Lake Chitu prokaryotes that have adapted to life styles in the harsh soda lake environments. Pathway analysis using KEGG metabolic maps of the Fosmid DNA sequences evidenced that the microorganisms Burkholderiales, Delftia acidovorans SPH-1, Achromobacter, Comamonadaceae, Ralstonia, and Bordetella, within the Betaprotobacteria in Lake Chitu majorly play roles in many ways of Methane, Nitrogen, Sulfur, and Carbon cycles.



Environmental bacteria are culturable