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Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

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...

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Autores principales: Kambura, Anne Kelly, Mwirichia, Romano Kachiuru, Kasili, Remmy Wekesa, Karanja, Edward Nderitu, Makonde, Huxley Mae, Boga, Hamadi Iddi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936230/
https://www.ncbi.nlm.nih.gov/pubmed/27388368
http://dx.doi.org/10.1186/s12866-016-0748-x
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author Kambura, Anne Kelly
Mwirichia, Romano Kachiuru
Kasili, Remmy Wekesa
Karanja, Edward Nderitu
Makonde, Huxley Mae
Boga, Hamadi Iddi
author_facet Kambura, Anne Kelly
Mwirichia, Romano Kachiuru
Kasili, Remmy Wekesa
Karanja, Edward Nderitu
Makonde, Huxley Mae
Boga, Hamadi Iddi
author_sort Kambura, Anne Kelly
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-016-0748-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-49362302016-07-07 Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya Kambura, Anne Kelly Mwirichia, Romano Kachiuru Kasili, Remmy Wekesa Karanja, Edward Nderitu Makonde, Huxley Mae Boga, Hamadi Iddi BMC Microbiol Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-016-0748-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-07-07 /pmc/articles/PMC4936230/ /pubmed/27388368 http://dx.doi.org/10.1186/s12866-016-0748-x Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Kambura, Anne Kelly
Mwirichia, Romano Kachiuru
Kasili, Remmy Wekesa
Karanja, Edward Nderitu
Makonde, Huxley Mae
Boga, Hamadi Iddi
Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
title Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
title_full Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
title_fullStr Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
title_full_unstemmed Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
title_short Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
title_sort bacteria and archaea diversity within the hot springs of lake magadi and little magadi in kenya
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936230/
https://www.ncbi.nlm.nih.gov/pubmed/27388368
http://dx.doi.org/10.1186/s12866-016-0748-x
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