Metagenomic Exploration Of Ethiopian Soda Lake Sediments Microbial Diversity And Community Structure

It is estimated that less than 1% of all known environmental bacteria are culturable. It is currentlyrnbelieved that the uses of genetic approaches including metagenomics can bypass culturing ofrnmicroorganisms and allow the identification of novel gene sequences and complete metabolic pathwaysrnof unculturable microorganisms directly from the environment.rnIn this study, 16S- rRNA-based metagenomics was used to investigate the microbial communityrncomposition and phylogenetic relationships of Chitu, Shalla and Abijata soda lakes in the Ethiopian RiftrnValley. Four 16S- rRNA-clone libraries were constructed for Chitu and Shalla lakes by usingrnenvironmental DNA from sediment samples and 16S rRNA primers specific to bacterial andrnactinobacterial domains. In addition, 454-pyrosequencing was used to identify microbial phylogeny andrncompositions of Chitu, Shalla and Abijata soda lakes using the V3-V4 hypervariable specific regions ofrnthe bacterial 16S-rRNA genes with bar-coding strategy. Moreover, metagenomic approaches were used tornconstruct a 40Kb fosmid (pCC1FOS vector) metagenomic DNA library of Chitu Soda Lake. Potentialrnenzymes, metabolic genes and pathways were detected using functional and sequence- basedrnmetagenomic.rn16S rRNA clone sequences of Chitu and Shalla Lakes were related to low and high G+C Gram-positivernbacteria (Firmictes and Actinobacteria), CFB, and Protobacteria of the γ-, α-, ß- and Δ-rnProteobacteria subdivisions. Most of the clones were phylogenetically allied with members of the γ-rnsubdivision of Protobacteria (accounted for 34–43% of sequences), followed by Firmicutes (affiliatedrnsequences at 16–26%). Both lakes were found to harbor biotechnologically and ecologically significantrnrepresentatives of microbes that belong to the members of the group Rhodobaca, Alkalimonas,rnNitrinicola, Thioalkalivibrio, Methylophaga, Desulfuromusa, Bacillus, Clostridium, Dethiobacter,rnCytophagales, Actinobacteria, and Bacteroidetes. Barcode- tagged 454 pyrosequencing of prokaryoticrncommunity of Chitu, Shalla, and Abijata soda lakes revealed much wider diversity and novelrnrepresentatives of microbial species that mostly included the methanogenic archaea (Methanocalculus),rnmethane-oxidizing (Methylomicrobium sp.), Cyanobacteria, photosynthetic purple bacteriarn(Halorhodospira), non-sulfur purple bacterial genera (Rhodobaca), SOB (Thioalkalivibrio,rnThioalkalispira, Sulfurimonas), SRB (Desulfobacterium, Desulfosarcina, Desulfurivibrio,rnDesulfonatronovibrio), Actonobacteria, Anoxybacillus, Bacillus, Clostridia, Nitrospira, Paracoccus,rnRhodobacteraceae, Pseudomonas, Bacteroidetes, Deinococcus-Thermus, Planctomycetes, andrnSpirochetes.rnA total of 288 Mb metagenomic DNA Fosmid library size was constructed from Lake Chitu sediments inrnEthiopian Rift Valley area. The plate screening of 7, 200 of total Fosmid clones of the lake sedimentsrnresulted significant proteolytic, amylolytic, cellulosic enzyme activities. Besides, sequence-basedrnfunctional analysis of Lake Chitu Fosmid DNA using Hiseq 2000 (Illumina) provided novel Lake Chiturnprokaryotes that have adapted to life styles in the harsh soda lake environments. Pathway analysis usingrnKEGG metabolic maps of the Fosmid DNA sequences evidenced that the microorganismsrnBurkholderiales, Delftia acidovorans SPH-1, Achromobacter, Comamonadaceae, Ralstonia, andrnBordetella, within the Betaprotobacteria in Lake Chitu majorly play roles in many ways of Methane,rnNitrogen, Sulfur, and Carbon cycles.

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