Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya

Abstract

Background Soda lakes are habitats characterized by haloalkaline conditions also known to host unique microbial communities. The water chemistry changes with seasons due to evaporative concentration or floods from the surrounding grounds. However, it is not yet clear if the change in physiochemical changes influences the spatiotemporal diversity and structure of microbial communities in these ecosystems. Methods This study investigated the spatiotemporal diversity and structure of microbial communities in water and brine samples collected from hypersaline Lake Magadi in the months of June–September 2018. Amplicons were generated using Illumina sequencing of the 16S rRNA gene. Results The abundant bacterial phyla were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Verrumicrobia, Deinococcus-Thermus, Spirochaetes, and Chloroflexi. The Archaeal diversity was represented by phyla Euryachaeota, Crenarchaeota, Euryarchaeota, and Thaumarchaeota. The dominant bacterial species were: Euhalothece sp. (10.3%), Rhodobaca sp. (9.6%), Idiomarina sp. (5.8%), Rhodothermus sp. (3.0%), Roseinatronobacter sp. (2.4%), Nocardioides sp. (2.3%), Gracilimonas sp. (2.2%), and Halomonas sp. (2%). The dominant archaeal species included Halorubrum sp. (18.3%), Salinarchaeum sp. (5.3%), and Haloterrigena sp. (1.3%). The composition of bacteria was higher than that of archaea, while their richness and diversity varied widely across the sampling seasons. The α-diversity indices showed that high diversity was recorded in the month of August, followed by September, June, and July in that order. Furthermore, salinity and alkalinity affect β-diversity rather than the sampling site or seasonality. The effects of physicochemical parameters on the microbial community structure showed that temperature, pH, P+, K+, NO3 -, and total dissolved solids (TDS) had a positive correlation with the microbial community structure. Multivariate analysis revealed significant spatial and temporal effects on β-diversity and salinity and alkalinity were the major drivers of microbial composition in Lake Magadi. Conclusions We provide insights into the relationships between microbial communities and geochemistry across various sampling sites in Lake Magadi.