Genetic Diversity of Actinobacteria Isolated from Lake Magadi

Abstract

Actinobacteria are morphologically and phylogenetically diverse Gram positive bacteria generally aerobic and have high genomic guanine-plus-cytosine (G+C) contents (>55 mol %). Many studies on alkaliphilic microbial communities have been done on Kenyan soda lakes focusing on general microbial diversity. However, actinobacterial communities have not been documented on Lake Magadi, a hyper saline lake with up to 34% salinity levels. Four different sampling points were selected randomly within the lake to cover a broad range of sample diversity. Sediments and water samples were collected from each sampling point. Serially diluted samples were plated on alkaline growth media containing complex substrates such as malt and chitin. The media was prepared using filtered lake water. DNA was extracted from the isolates and the 16S rRNA genes amplified using primers described to be domain specific for actinobacteria. The PCR based method was used to screen actinobacteria from other isolates. Eleven isolates produced amplifications and were presumed to be actinobacteria and thus characterized further. The amplified products were used for sequence analysis. Five actinobacteria isolates were obtained belonging to the families Norcadiaceae, Microbactericeae, Streptomycetaceae and Dietziaceae. BLAST analysis showed that isolates MS-2, MS-3, MS-5, MM-10 and MS-11 had between 97% to 99% similarity to their close relatives. The isolates were affiliated with the genera Dietzia, Microbacterium, Rhodococcus, Streptomycetes xv and Nocardia respectively. Screening of the isolates for type-1 polyketide synthases showed isolates MS-1, MS-2, MS-5, MS-9, MM-10 and MS-11 to contain these biosynthetic systems involved in synthesis of biologically active compounds. All the domains obtained had below 80% identity to GenBank sequences. This may imply chemical and functional novelty. The isolates were characterized both physiologically and biochemically and were tested for production of extra-cellular enzymes. The physiological results from the study showed that growth was possible up to a pH of 11. Isolates MS-2, MS-5, MSL-7, MM-9, MM-10, and MS-11 were alkaliphiles and isolates MS-1, MS-3, MS-4 and MM-8 were alkalitolerants. Optimum growth temperature was at 30°C and the highest at 40°C. All isolates were able to grow in media with Sodium chloride. Eight isolates grew optimally at 5% w/v salt and the rest in media without salt. The isolates were able to utilize various carbon sources and produced hydrolytic enzymes such as lipase, amylase, xylanase, proteinase and cellulase. They showed antagonistic activity against both Gram negative and Gram positive bacteria. These findings show that isolates from Lake Magadi are metabolically active and adapted to life in the alkaline environment.