Abstraction Method Shapes Microbial Ecology and Pathogen Risk in Water from Shallow Aquifers

Shallow groundwater is a vital water source in semi-arid regions, where wet season recharge can be naturally filtered and stored, protected from evaporation, for year-round use. However, communities in these regions continue to suffer from a high prevalence of preventable diseases transmitted by waterborne pathogens. This study applies ecological theory to address critical knowledge gaps in our understanding of the microbial ecology of groundwater systems. We use quantitative PCR and 16S rRNA gene sequencing to characterize pathogenic indicator species and bacterial communities around three isolated aquifers formed by sand dams in southeast Kenya. Samples were compared across multiple seasons and abstraction methods used by local communities, including sealed hand pumps (classified by the WHO as an improved source), open wells, scoop holes, and downstream surface water.