Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
Identifieur interne : 000050 ( Main/Merge ); précédent : 000049; suivant : 000051Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya
Auteurs : Anne Kelly Kambura [Kenya] ; Romano Kachiuru Mwirichia [Kenya] ; Remmy Wekesa Kasili [Kenya] ; Edward Nderitu Karanja [Kenya] ; Huxley Mae Makonde [Kenya] ; Hamadi Iddi Boga [Kenya]Source :
- BMC Microbiology [ 1471-2180 ] ; 2016.
Abstract
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.
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
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:
There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (
The online version of this article (doi:10.1186/s12866-016-0748-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12866-016-0748-x
PubMed: 27388368
PubMed Central: 4936230
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya</title>
<author><name sortKey="Kambura, Anne Kelly" sort="Kambura, Anne Kelly" uniqKey="Kambura A" first="Anne Kelly" last="Kambura">Anne Kelly Kambura</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi</wicri:regionArea>
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<author><name sortKey="Mwirichia, Romano Kachiuru" sort="Mwirichia, Romano Kachiuru" uniqKey="Mwirichia R" first="Romano Kachiuru" last="Mwirichia">Romano Kachiuru Mwirichia</name>
<affiliation wicri:level="1"><nlm:aff id="Aff2">Embu University College, P. O. Box 6-60100, Embu, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Embu University College, P. O. Box 6-60100, Embu</wicri:regionArea>
<wicri:noRegion>Embu</wicri:noRegion>
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<author><name sortKey="Kasili, Remmy Wekesa" sort="Kasili, Remmy Wekesa" uniqKey="Kasili R" first="Remmy Wekesa" last="Kasili">Remmy Wekesa Kasili</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
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<wicri:noRegion>Nairobi</wicri:noRegion>
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<author><name sortKey="Karanja, Edward Nderitu" sort="Karanja, Edward Nderitu" uniqKey="Karanja E" first="Edward Nderitu" last="Karanja">Edward Nderitu Karanja</name>
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<wicri:regionArea>International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi</wicri:regionArea>
<wicri:noRegion>Nairobi</wicri:noRegion>
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<author><name sortKey="Makonde, Huxley Mae" sort="Makonde, Huxley Mae" uniqKey="Makonde H" first="Huxley Mae" last="Makonde">Huxley Mae Makonde</name>
<affiliation wicri:level="1"><nlm:aff id="Aff4">Pure and Applied Sciences, Technical University of Mombasa, P. O. Box 90420-80100, GPO, Mombasa, Kenya</nlm:aff>
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<wicri:noRegion>Mombasa</wicri:noRegion>
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</author>
<author><name sortKey="Boga, Hamadi Iddi" sort="Boga, Hamadi Iddi" uniqKey="Boga H" first="Hamadi Iddi" last="Boga">Hamadi Iddi Boga</name>
<affiliation wicri:level="1"><nlm:aff id="Aff5">Taita Taveta University College, P.O. Box 635-80300, Voi, Kenya</nlm:aff>
<country xml:lang="fr">Kenya</country>
<wicri:regionArea>Taita Taveta University College, P.O. Box 635-80300, Voi</wicri:regionArea>
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<series><title level="j">BMC Microbiology</title>
<idno type="eISSN">1471-2180</idno>
<imprint><date when="2016">2016</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Methods</title>
<p>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 <italic>“Nasikie eng’ida”</italic>
(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.</p>
</sec>
<sec><title>Results</title>
<p>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: <italic>Proteobacteria</italic>
(8.33–50 %), <italic>Firmicutes</italic>
3.52–28.92 %, <italic>Bacteroidetes</italic>
(3.45–26.44 %), <italic>Actinobacteria</italic>
(0.98–28.57 %) and <italic>Euryarchaeota</italic>
(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).</p>
</sec>
<sec><title>Conclusion</title>
<p>There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (<italic>P</italic>
value, 0.009) based on 16S rDNA analysis and active microbial diversity (<italic>P</italic>
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.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12866-016-0748-x) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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