Isolation and Characterization of extreme haloalkaliphilic Bacteria and Archaea from Lake Magadi, Kenya.

Abstract

A variety of microbes inhabit extreme environments normally unsuitable for life such as soda lakes. Soda lake microbes have attracted attention as a possible source of novel enzymes and metabolites for use in biotechnology and are much sought for possible biotechnological use. This is because of their ability to survive and function under severe conditions comparable to those prevailing in various industrial processes. Halophiles in particular, have been cultured and screened for molecules of industrial interest that include extremoenzymes, compatible solutes and biopolymers from different hypersaline environments, including the Kenyan soda lakes. However, very little has been documented on Lake Magadi, which is not only hypersaline but also alkaline (with up to 30% salinity and 12.5 pH levels). This work aimed at isolating, characterizing and screening extremophiles from Lake Magadi for the ability to produce useful biotechnological enzymes. Isolation was done using media of two different categories (Mineral rich and Carbon rich media). Characterization of the isolates was done using cultural, biochemical and molecular approaches while their screening for the ability to produce extracellular enzymes was done by plating them on basal media supplemented with the respective substrate.

A total of 37 isolates were recovered from Lake Magadi of which 34 were Gram positive, one was Gram negative and two were Gram variable. The majority grew well at pH ranging from 6.0 – 11.0, (optimum 9.0-10.0), temperature range of 20 –45 oC (optimum of 30-35 oC) and salinity range of 5- 30 %, optimum growth was noted at 10-15%. 15 isolates produced various extracellular enzymes such as amylases, lipases and proteases. Blast analysis of the partial sequences revealed that the study recovered bacteria affiliated to genera Bacillus, Clostridium and Halomonas from this lake, with relative abundances of 54%, 38% and 8% respectively. Isolates G-15, G-2, G-11, G-18, S-10, S-12, D-9, C-13, M6-1, C-3, X-6, S-3, M8-14, C-4, D-2, D-6, M8-12, S-11, M8-11 and C-1 clustered with members of genera Bacillus with different similarity scores ranging between 98–100%. Isolates S-2, M8-15, G-8, G-4, X-2, M6-7, S-7, G-20, C-6, C-5, G-14, G-12 and X-3 clustered with members of genus Clostridium with similarity values ranging between 80% and 99% while only isolate X-5 clustered with genus Halomonas with a similarity score of 94%. The similarity values of isolates C-6, G-12 and X-5 (94% - 97%) and those of isolates X-3 (88%), G-14 (80%), C-1 (78%), C-5 (84%) and G-20 (85%) to their closest relatives show that these could represent new species and novel genera repectively within the lake ecosystem. This study therefore reports that extreme haloalkaliphilic bacteria constitute a significant part of the microbiota that inhabit Lake Magadi, which have the ability to produce biotechnologically useful enzymes, and recommends more studies to widen the diversity of cultured microbes, use of more media types and different protocols that may increase the range of enzymes produced, and further characterization of the enzymes.