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Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg2+) and sulfate (SO42−), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO42−, Mg2+ and Na+. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.
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•Prokaryotes are rarely considered in environmental assessments.•Metabarcoding was used to assess mine-water impacts on groundwater prokaryotes.•Saline mine-waters altered prokaryote community composition and function.•Changes were strongly correlated with elevated concentrations of SO42+, Mg+ and Na+.
Saline mine-waters with elevated concentrations of SO42−, Mg2+ and Na + resulted in changes in prokaryote community composition and functional processes.