Isolation and characterization of extremophilic bacteria from the hot springs of Lake Magadi, Kenya

Abstract

Hot springs are aquatic environments with extremely high temperatures. They harbor a group of extremophiles called haloalkaliphilic bacteria that have developed mechanisms to thrive at high temperature, pH and salinity conditions comparable to those prevailing in various industrial processes. Research on these microbes has been motivated by their great biotechnological potential such as production of useful secondary metabolites and extremozymes with industrial application. Isolation, characterization and identification of haloalkaliphilic bacteria have been done on Kenyan soda lakes. However, more information about the hot springs of Lake Magadi, a hyper saline lake with up to 30 w/v % salinity, 12.5 pH levels and 86°C is needed. This work was aimed at isolating, characterizing and screening extremophiles from Lake Magadi hot springs for the ability to produce useful biotechnological enzymes. Collection of water, wet sediments and microbial mats was carried out from the springs in the main lake at a temperature of 45.1°C and from Little Magadi Nasikie eng’ida (temperature of 81 and 83.6°C). A total of 44 bacteria isolates were recovered using selective media prepared with filter-sterilized water from the lake. These were characterized using morphological, physiological, biochemical and molecular approaches. The isolates were also screened for production of extracellular enzymes and antimicrobial activity. Majorities (80%) of bacteria isolated were Gram positive and few (20%) were Gram negative. They grew well at pH range of 6 –14(optimum 9-12), temperature range of 30 – 60°C (optimum 40-50°C) and sodium chloride (salt)range of 0- 15 % (optimum 0-7.5%). The bacterial isolates produced various extracellular enzymes such as amylases, cellulases, proteases, lipases and esterases. Antimicrobial assays done against test organisms (bacteria and fungi) showed that the isolates had range of inhibitory effects. All isolates produced various colored pigments in the media indicating that they could be a source of diverse bioactive metabolites. Bacterial DNA was extracted using phenol-chloroform extraction method and isopropyl alcohol precipitation method. Nearly full-length 16S rRNA gene sequences were PCR amplified using forward bacterial Primer 8F and reverse bacterial primer 1492R to get 1500 bp of the PCR product. Sequencing of the 16S rDNA of the isolates was done and sequences for 7 isolates were without ambiguities. BLAST results revealed that the isolates belonged to domain bacteria, 90% of isolated microbes had an affiliation to phylum Firmicutes, class Bacilli, order Bacillates, family Bacillaceae and genus Bacillus while 10% was affiliated to phylum Proteobacteria, class Betaproteobacteria, Order Burkholderiales, family Alcaligenaceae and genus Alcaligenes. Isolates HS3, HS10, HS13, HS18, HS29 and HS41clustered with members of genus Bacillus with similarity scores ranging between 86%–98%, while isolate HS28 clustered to genus Alcaligenes with 96% sequence similarity. Strains from Bacillus family included; Bacillus siamensis, Bacillus licheniformis, Bacillus methylotrophicus, Bacillus amyloliquefaciens, Bacillus pumilus, and Bacillus sonorensis while one strain that belonged to Alcaligenes family was Alcaligenes feacalis. Based on the results, the isolates recovered were halotolerant, alkalitolerant and thermotolerant. This study demonstrates that extreme environments of the hot springs of Lake Magadi harbor extremophilic bacteria with the potential to produce enzymes and antimicrobial compounds. Further research should focus on different protocols and novel microbial culture techniques which allow the identification of a bigger diversity of genera accompanied by extensive research on the specific secondary metabolites released by extremophiles from Lake Magadi hot springs.