| dc.description.abstract | Background: Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan
Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C.
Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms
thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but
were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of
amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure
of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi.
Methods: Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature
of 45.1 °C and from Little Magadi “Nasikie eng’ida” (temperature of 81 °C and 83.6 °C). Total community DNA and
RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The
16S rRNA gene variable region (V4 – V7) of the extracted DNA and RNA were amplified and library construction
performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of
Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS)
redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the
Vegan package.
Results: Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered
from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35 % 16S rDNA and 87.61 %
16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included:
Proteobacteria (8.33–50 %), Firmicutes 3.52–28.92 %, Bacteroidetes (3.45–26.44 %), Actinobacteria (0.98–28.57 %) and
Euryarchaeota (3.55–34.48 %) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three
groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters
between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot
spring (45.1 °C) contained less diverse populations compared to those in Little Magadi (81–83 °C).
Conclusion: There were significant differences in microbial community structure at 95 % level of confidence for
both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based
on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were
observed as a function of sample type and temperature, with wet sediments harboring the highest diversity. | en_US |
