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: 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.

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 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.

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

Keywords: Soda lake; archaea; bacteria; physicochemical parameters; spatiotemporal; α-diversity; β-diversity.

Figure 1.. Map of Lake Magadi showing the sampling sites.

Figure 2.. Alpha diversity plots of OTU richness among different sampling months.

Figure 3.. Principal component analysis (PCA) ordination of differences in microbial communities from sampling sites and sampling months.

Figure 4.. Relative abundance and composition of the microbial community taxa based on sampling sites and month of sampling.

(A) The proportion of Domains bacteria and archaea across the sampling sites and months. (B) Relative abundance of the most popular bacterial and archaeal phyla across the sampling sites and the sampling months.

Figure 5.. Read abundance (%) of the top 30 species across samples.

Figure 6.. Network analysis of microbial community at Family level based on sampling sites.

Samples marked with red squares indicate their exclusive site of isolation.

Figure 7.. Redundancy Analysis (RDA) ordination showing the relationships between the physicochemical factors and the dominant genera in Lake Magadi. Samples corresponding to their sampling month are indicated, while genera are written in red, and environmental variables are indicated by arrows. TDS corresponds to total dissolved solids.