Microbial Diversity of Lake Elmenteita, Kenya

Abstract

The major goal of microbial ecology is to understand microbial diversity in naturalhabitats their interaction with one another and with their habitat. The soda lakes arehighly productive environments and the soda lakes of the East African Rift valleyhave been shown to support a dense and diverse population of aerobic,organotrophic, halophilic, alkaliphilic and alkalitolerant representatives of majorbacterial and archaeal phyla.The isolation and characterization of organisms belonging to widespread butpreviously uncultivated groups of organisms can provide insights into the roles andfunctions of these organisms in their natural settings and assist in the formulationof hypotheses about metabolic interactions between microorganisms and theirnatural environment. Several studies have been carried out to document themicrobial diversity of the Kenyan soda lakes by other researchers. However nocomprehensive study has been done in Lake Elmenteita. The aim of this study wasto assess the microbial diversity of Lake Elmenteita using both culture independentand culture dependent techniques. The application of both techniques was expectedto provide new insights into the microbial diversity of the Lake as well as possibleroles played by each group within the soda lake environment.Application of molecular tools to study microbial ecology has widened ourapproximation of diversity in the environments. Clone Libraries were constructedfrom PCR amplicons from total environmental DNA. Primers specific for Bacteriaand Archaea respectively were used. Partial sequences were generated for both theclones and the isolates. The relatedness of the Lake Elmenteita bacterial rRNAsequences to known rRNA gene sequences was determined by BLAST analysisand by alignment to the sequences on the ARB database (Release, 1994).Clones possessed a higher similarity to other environmental clones than to culturedmicroorganisms. A total of 655 clone sequences were sequenced. Of these 525(80.15%) sequences were related to uncultured members of the Domain Bacteria.This indicates that a large proportion of deep phylogenetic groups are representedin the clone libraries. Sixteen percent of the clones had similarity values below90% to both cultured and uncultured microorganisms. Forty three percent of theclones had similarity values between 90-95% as compared to 34.35% that hadvalues between 96-98%. Only a mere 6.87% had values between 99-100%.However a number of factors including relatively low cell numbers of largeorganisms and a variable number of rRNA operons among organisms, as well asextraction and PCR bias, may lead to under-representation of phylotypes relative totheir in situ abundance.Cultured isolates are still very important in developing our understanding ofbacterial physiology, genetics, and ecology. Isolation was done using both nutrientrich and nutrient poor media. A polyphasic approach was employed in theidentification of the various strains. The majority of the isolates (36.75%) belongedto the genus Halomonas while 31.35% belonged to the Genus Bacillus. More thanhalf of the isolates (59.45%) belonged to the Gammaproteobacteria. An overlapbetween the clone library and the isolates was observed in the Order Bacillales andthe Actinobacteria only. In this study novel isolates related to Marinospirillum,Idiomarina, Streptomyces, _ocardia, Marinilactibacillus, Amphibacillus andVibrio were recovered. A polyphasic approach to characterization showed theyrepresented novel taxa.The study showed that the application of both culture dependent and cultureindependent methods gives a better picture of diversity in the environment. It canbe concluded the soda lakes harbour novel uncultured groups of microorganismsand most of them are of biotechnological potential. Future work should focus onArchaeal diversity as well as the uncultured groups of bacteria.