Browsing by Author "Kambura, Anne Kelly"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya
    (PLOS, 2020-08) Karanja, Edward N.; Fliessbach, Andreas; Adamtey, Noah; Kambura, Anne Kelly; Musyoka, Martha; Fiaboe, Komi; Mwirichia, Romano K.
    Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial populations. In this study, we investigated the effect of conventional versus organic farming systems at low and high input levels on structure and diversity of prokaryotic microbial communities. Soil samples were collected from the ongoing long-term farming system comparison trials established in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample were analyzed. Total DNA and RNA amplicons of variable region (V4—V7) of the 16S rRNA gene were generated on an Illumina platform using the manufacturer’s instructions. Diversity indices and statistical analysis were done using QIIME2 and R packages, respectively. A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97% genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely, while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria and Acidobacteria. Conventional farming systems showed a higher species richness and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets were similar. Physiochemical factors were associated differently depending on rRNA and rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc, iron, boron and micro-aggregates showed a significant influence on the observed microbial diversity. The observed higher species diversity in the conventional farming systems can be attributed to the integration of synthetic and organic agricultural inputs. These results show that the type of inputs used in a farming system not only affect the soil chemistry but also the microbial population dynamics and eventually the functional roles of these microbes.
  • Thumbnail Image
    Item
    Isolation and Characterization of Bacteria from Lakes Olbolosat and Oloiden, Kenya
    (Academic journals, 2020) Kiama, Catherine Wachera; Njire, Moses Mucugi; Kambura, Anne Kelly; Matiru, Viviene Njeri; Wafula, Eliud Nalianya; Mugweru, Julius Ndirangu; Mugweru, Julius Ndirangu
    There is still unexplored reservoir of microorganisms from sediments and water within Lakes Olbolosat and Oloiden using culture dependent technique. The current study compares bacterial diversity within Lake Olbolosat a freshwater lake and Lake Oloiden a saline alkaline lake. Out of 60 isolates obtained from sediments and water samples, 35 were from Lake Olbolosat and 25 from Lake Oloiden. Microbial count ranged between 0-1.75× 10 5 cfu/ml from both lakes. There was a significant difference between bacterial density and sampling points (p<0.001, F=6.667), 58 were Gram-positive and 2 Gram-negative. Fifty-five isolates that were rod-shaped, 3 were cocci and 2 filamentous. There was excellent growth of isolates at an optimum growth pH range of 6-10, a temperature range of 25-30°C and a salinity range of 0-5%. There was significant difference at p<0.001 for bacterial growth within physiological parameters. The isolates utilized skimmed milk, starch, olive oil, cellulose powder and xylan, hence the production of extracellular enzymes. There was antimicrobial activity against Pseudomonas aeruginosa, Bacillus subtilis, Escherichia coli, Staphylococcus aureus and Candida albicans by bacterial isolates. BLAST analysis of partial sequences showed there were 4 different phyla. Firmicutes scored 77% closely affiliated with 20 strains, Actinobacteria scored 15% closely affiliated with 4 strains, Proteobacteria and Bacteroidetes scored 4% affiliated with 1 strain each. Novel bacteria from this study could provide insights into their diversity and biotechnological applications.