Microbial Diversity and Community Structure within Equatorial Lakes Olbolosat and Oloiden in Kenya

Abstract

Lakes Olbolosat and Oloiden which lies along the equator are economically and ecologically important ecosystems due to their high productivity and nutrient recycling capacities. Microbes are important in the functioning and stability of lake ecosystems. Due to the complexity of the culture-dependent techniques, only a limited number of microbes have been extensively studied. Metagenomics therefore, provides detailed information on the studies of microbial communities for microbes that cannot be isolated using culture-dependent technique. This is the first comprehensive study to study microbial diversity and community structure within Equatorial lakes Olbolosat and Oloiden in Kenya. Culture-dependent technique targeted 16S rRNA gene for the identification of bacterial isolates with lakes Olbolosat and Oloiden. High throughput sequencing was performed on 15 samples obtained from the two lakes using the Illumina Miseq platform. Four different Phyla: Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes were recovered using a culture-dependent technique. Firmicutes were predominant within the two lakes. There were 17 and 10 phyla recovered using the culture-independent for the bacteria and fungi respectively. The abundant phyla included Proteobacteria (33.8 %), Firmicutes (27.3 %), Actinobacteriota (21.2 %), Chloroflexi (6.8 %), Cyanobacteria (3.8 %), Acidobacteriota (2.8 %), Planctomycetota (1.9 %) and Bacteroidota (1.1 %). Analysis of similarity (ANOSIM) revealed a significant difference in ASV composition between the two lakes (r = 0.191, p = 0.048), and between the sample types (r = 0.6667, p = 0.001). The analysis of the ITS ASVs comprised of the fungi kingdom (73.1 %) and Plantae kingdom (28.7 %), the microalgae photobionts. Among the ten highly abundant phyla, two (Chlorophyta; 56.87 % and Anthophyta; 1.2 %) belonged to kingdom Plantae, while eight (Mortierellomycota; 17.8%, Basidiomycota; 11.8 %, Chytridiomycota; 5.8 %, Monoblepharomycota; 3.4 %, Ascomycota; 2.4 %, Olpidiomycota; 0.5 %, Mucoromycota; 0.1 %, and Glomeromycota; 0.1 %) belonged to kingdom fungi. Chlorophyta (56.87 %) was the predominant phyla across the samples except for the dry sediments in both lakes that were dominated by phylum Mortierellomycota. An evaluation of the indicator ASVs correlation at the phylum level revealed a positive co-occurrence pattern among the genera of the ten major phyla for both bacteria and fungi. The interaction network for the bacterial and fungal communities within the two lakes displayed the predominant phyla to be highly positively connected with other microbes. The findings show that the microbial communities were influenced by environmental factors within the tow lakes. Lake Olbolosat a fresh water body harbored a high number of microbial taxa as compared to Lake Oloiden which is a saline-alkaline water body. Targeted bacterial and fungal isolation should be carried out to recover, characterize and identify the recovered novel microbial taxa revealed through next-generation sequencing. Novel bacteria recovered from this study could provide insights into their diversity and biotechnological applications.