Microbial communities and their predicted metabolic functions in a desiccating acid salt lake

Abstract

The waters of Lake Magic in Western Australia are among the most geochemically extreme on Earth. This ephemeral saline lake is characterized by pH as low as 1.6 salinity as high as 32% total dissolved solids, and unusually complex geochemistry, including extremely high concentrations of aluminum, silica, and iron. We examined the microbial composition and putative function in this extreme acid brine environment by analyzing lake water, groundwater, and sediment samples collected during the austral summer near peak evapoconcentration. Our results reveal that the lake water metagenome, surprisingly, was comprised of mostly eukaryote sequences, particularly fungi and to a lesser extent, green algae. Groundwater and sediment samples were dominated by acidophilic Firmicutes, with eukaryotic community members only detected at low abundances. The lake water bacterial community was less diverse than that in groundwater and sediment, and was overwhelmingly represented by a single OTU affiliated with Salinisphaera. Pathways associated with halotolerance were found in the metagenomes, as were genes associated with biosynthesis of protective carotenoids. During periods of complete desiccation of the lake, we hypothesize that dormancy and entrapment in fluid inclusions in halite crystals may increase long-term survival, leading to the resilience of complex eukaryotes in this extreme environment.

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Acknowledgements

We thank Yi Cui (Missouri S&T) for assistance with DNA extraction. This work was supported by an Experimental Program to Stimulate Competitive Research at the National Aeronautics and Space Administration, Missouri Research Infrastructure Development award (M.M.), a Georgetown University Main Campus Research Fellowship (S.S.J. and E.Z.), and West Virginia University (K.B.).

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Communicated by A. Oren.

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Supplementary Fig. 1. Taxonomic composition and diversity of bacterial SSU rRNA gene OTUs (97% ID). Krona charts showing the relative abundance of each bacterial taxon identified in the Lake Magic samples. Within each chart, circles are arranged hierarchically, with the innermost circle corresponding to phylum and outermost circle representing genus. LW = lake water, GW = groundwater, and SS = subaqueous sediment (PDF 923 kb)

Supplementary Fig. 2. Taxonomic composition and diversity of Lake Magic metagenomic reads. (a) Krona charts showing the relative abundance of bacterial phyla identified in the Lake Magic samples. The PVC clade includes the phyla Chlamydiaea, Lentisphaerae, Planctomycetes, and Verrucomicrobia, the FCB group encompasses the Chlorobi, Bacteroidetes and Fibrobacteres phyla, and the Terrabacteria group includes the Actinobacteria, Deinococcus–Thermus, Cyanobacteria, Chloroflexi, and Firmicutes. (b) Krona charts showing the relative abundance of eukaryotic phyla identified in the Lake Magic samples. LW = lake water, GW = groundwater, and MFS = mudflat sediment (PDF 866 kb)

Supplementary Fig. 3. Distribution of Lake Magic metagenomic read assignments to SEED subsystems. Bars represent the total number of reads assigned to each subsystem. LW = lake water (green), GW = groundwater (blue), and MFS = mudflat sediment (purple) (PDF 872 kb)

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Zaikova, E., Benison, K.C., Mormile, M.R. et al. Microbial communities and their predicted metabolic functions in a desiccating acid salt lake. Extremophiles 22, 367–379 (2018). https://doi.org/10.1007/s00792-018-1000-4

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Keywords

  • Acid brine
  • Lake
  • Extremophiles
  • Polyextremophilic
  • Microbial communities
  • Fluid inclusions