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

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.

Using 16S rRNA gene amplicon sequencing, we investigated the diversity and structure of microbial communities in water and brine samples taken from Lake Magadi between June and September 2018. Additionally, physicochemical parameters were also analyzed for every sampling site. Additionally, physicochemical parameters were also analyzed for every sampling site.

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 August, followed by September, June, and July in that order. The findings demonstrated that temperature, pH, P+, K+, NO3 -, and total dissolved solids (TDS) contributed majorly to the diversity observed in the microbial community. 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.

We provide insights into the relationships between microbial structure and geochemistry across various sampling sites in Lake Magadi.