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Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya.
BMC Microbiol. 2016 07 07; 16(1):136.BM

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.

Authors+Show Affiliations

Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.Embu University College, P. O. Box 6-60100, Embu, Kenya.Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi, Kenya.Pure and Applied Sciences, Technical University of Mombasa, P. O. Box 90420-80100, GPO, Mombasa, Kenya.Taita Taveta University College, P.O. Box 635-80300, Voi, Kenya. hamadiboga@ttuc.ac.ke.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27388368

Citation

Kambura, Anne Kelly, et al. "Bacteria and Archaea Diversity Within the Hot Springs of Lake Magadi and Little Magadi in Kenya." BMC Microbiology, vol. 16, no. 1, 2016, p. 136.
Kambura AK, Mwirichia RK, Kasili RW, et al. Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiol. 2016;16(1):136.
Kambura, A. K., Mwirichia, R. K., Kasili, R. W., Karanja, E. N., Makonde, H. M., & Boga, H. I. (2016). Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiology, 16(1), 136. https://doi.org/10.1186/s12866-016-0748-x
Kambura AK, et al. Bacteria and Archaea Diversity Within the Hot Springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiol. 2016 07 7;16(1):136. PubMed PMID: 27388368.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. AU - Kambura,Anne Kelly, AU - Mwirichia,Romano Kachiuru, AU - Kasili,Remmy Wekesa, AU - Karanja,Edward Nderitu, AU - Makonde,Huxley Mae, AU - Boga,Hamadi Iddi, Y1 - 2016/07/07/ PY - 2015/12/30/received PY - 2016/06/15/accepted PY - 2016/7/9/entrez PY - 2016/7/9/pubmed PY - 2017/6/7/medline KW - 16S rDNA KW - 16S rRNA cDNA KW - Hot springs KW - Lake Magadi KW - Microbial diversity SP - 136 EP - 136 JF - BMC microbiology JO - BMC Microbiol VL - 16 IS - 1 N2 - 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. SN - 1471-2180 UR - https://www.unboundmedicine.com/medline/citation/27388368/Bacteria_and_Archaea_diversity_within_the_hot_springs_of_Lake_Magadi_and_Little_Magadi_in_Kenya_ DB - PRIME DP - Unbound Medicine ER -