Browsing by Author "Boga, Hamadi Iddi"

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    Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
    (2016-07) Mwirichia, Romano K.; Kambura, Anne Kelly; Kasili, Remmy Wekesa; Karanja, Edward Nderitu; Makonde, Huxley Mae; Boga, Hamadi Iddi
    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.
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    Diversity of fungi in sediments and water sampled from the hot springs of Lake Magadi and Little Magadi in Kenya
    (2016-02) Mwirichia, Romano K.; Kambura, Ann K.; Kasili, Remmy W.; Boga, Hamadi Iddi; Karanja, Edward N.; Makonde, Huxley M.
    Lake Magadi and Little Magadi are saline, alkaline lakes lying in the southern part of Kenyan Rift Valley. Their solutes are supplied by a series of alkaline hot springs with temperatures as high as 86°C. Previous culture-dependent and independent studies have revealed diverse prokaryotic groups adapted to these conditions. However, very few studies have examined the diversity of fungi in these soda lakes. In this study, amplicons of Internal Transcribed Spacer (ITS) region on Total Community DNA using Illumina sequencing were used to explore the fungal community composition within the hot springs. Operational taxonomic units (OTUs) were analyzed using QIIME 1.8.0, taxonomy assigned via BLASTn against SILVA 119 Database and hierarchical clustering was done using R programming software. A total of 334, 394 sequence reads were obtained from which, 151 OTUs were realized at 3% genetic distance. Taxonomic analysis revealed that 80.33% of the OTUs belonged to the Phylum Ascomycota, 11.48% Basidiomycota while the remaining consisted of Chytridiomycota, Glomeromycota and early diverging fungal lineages. The most abundant Ascomycota groups consisted of Aspergillus (18.75%), Stagonospora and Ramularia (6.25% each) in wet sediment at 83.6°C, while Penicillium and Trichocomaceae (14.29% each) were dominant in wet sediment at 45.1°C. The results revealed representatives of thermophilic and alkaliphilic fungi within the hot springs of Lake Magadi and Little Magadi. This suggests their ability to adapt to high alkalinity, temperature and salinity.
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    Potential human pathogenic bacteria in five hot springs in Eritrea revealed by next generation sequencing
    (PLOS ONE, 2018-03) Ghilamicael, Amanuel M.; Boga, Hamadi Iddi; Anam, Sylvester E.; Mehari, Tadesse; Budambula, Nancy
    Human pathogens can survive and grow in hot springs. For water quality assessment, Escherichia coli or Enterococci are the main thermotolerant enteric bacteria commonly used to estimate the load of pathogenic bacteria in water. However, most of the environmental bacteria are unculturable thus culture methods may cause bias in detection of most pathogens. Illumina sequencing can provide a more comprehensive and accurate insight into environmental bacterial pathogens, which can be used to develop better risk assessment methods and promote public health awareness. In this study, high-throughput Illumina sequencing was used to identify bacterial pathogens from five hot springs; Maiwooi, Akwar, Garbanabra, Elegedi and Gelti, in Eritrea. Water samples were collected from the five hot springs. Total community DNA was extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4—V7) of the extracted DNA was amplified and library construction done according to Illumina sequencing protocol. The sequence reads (length >200 bp) from Illumina sequencing libraries ranged from 22,091 sequences in the wet sediment sample from Garbanabra to 155,789 sequences in the mat sample from Elegedi. Taxonomy was assigned to each OTU using BLASTn against a curated database derived from GreenGenes, RDPII, SILVA SSU Reference 119 and NCBI. The proportion of potential pathogens from the water samples was highest in Maiwooi (17.8%), followed by Gelti (16.7%), Akwar (13.6%) and Garbanabra (10.9%). Although the numbers of DNA sequence reads from Illumina sequencing were very high for the Elegedi (104,328), corresponding proportion of potential pathogens very low (3.6%). Most of the potential pathogenic bacterial sequences identified were from Proteobacteria and Firmicutes. Legionella and Clostridium were the most common detected genera with different species. Most of the potential pathogens were detected from the water samples. However, sequences belonging to Clostridium were observed more abundantly from the mat samples. This study employed high-throughput sequencing technologies to determine the presence of pathogenic bacteria in the five hot springs in Eritrea.
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    Thermotolerant bacteria of biotechnological potential from hot springs in Eritrea
    (2018-06) Ghilamicael, Amanuel M.; Budambula, Nancy; Anami, Sylvester E.; Mehari, Tadesse; Boga, Hamadi Iddi
    Thermophiles are excellent sources of enzymes that can withstand and carry out reactions efficiently under high temperatures. This study isolated and characterised thermotolerant bacteria that produce enzymes of potential industrial value from five hot springs in Eritrea. A total of 65 bacterial isolates were obtained from the five hot springs. Out of the 65 isolates; 19 isolates produced a positive reaction for amylases, 36 for carboxymethyl cellulases, eight for proteases, 10 for xylanases and 11 for pectinases. More than half (36 out of 65) were able to produce carboxymethyl cellulases. Six isolates which showed carboxymethyl cellulase activity were from the genus Bacillus, while those belonging to Brevibacillus were seven. BLAST analysis of the partial sequences showed that 19 out of the 24 isolates sequenced showed high similarity (> 99%) to those of reference strains of the genera Bacillus and Brevibacillus available in the Genebank and EZ-taxon databases. The five isolates (E5, G2, G8, M1 and M13) that showed moderate similarities (97.2-99%) to strains from the Genebank and EZ-taxon databases were further characterized. Physiological characterization of the five selected isolates based on tolerance to NaCl, temperature and production of hydrolytic enzymes indicated that these isolates are potentially novel. Isolates G8 and M13 showed significantly higher amylase activity (p < 0.05) than the other three isolates. Caseinase activity recorded by the five isolates was the highest (p < 0.05) compared to other enzyme activities. The enzymes produced by thermotolerant bacteria from the five hot springs may be potentially useful for catalysis under harsh operational conditions encountered in industrial processes.