Abstraction method shapes microbial ecology and pathogen risk in water from shallow aquifers

Abstract

Shallow groundwater in semi-arid regions provides a critical year-round water source, naturally filtered and protected from evaporation. However, many communities continue to suffer from preventable diseases caused by waterborne pathogens. This study applies ecological theory to investigate the microbial ecology of shallow aquifers in southest Kenya. We used quantitative PCR and 16S rRNA gene sequencing to characterize pathogenic indicator species and bacterial communities in three isolated sand dam aquifers across seasons and between various 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. Both faecal and opportunistic environmental pathogens were detected in all samples. However, our models indicate that contamination largely originates from unsealed abstraction points such as open wells and cracked hand pumps which expose water to the environment. In contrast, natural sand filtration effectively limited the dispersal of species between sample points. Abstraction method was the dominant factor shaping microbial community structure, exceeding seasonal or locational effects. Unimproved sources exhibited unstable, stressed ecosystems with reduced diversity and resilience, consistent with strong environmental selection pressures. Across all abstraction points, community composition reflected adaptation to local environmental niches that remained consistent between sites and seasons. Groundwater contained significantly fewer total microbes (16S rRNA copies) than surrounding surface water, and hand pump samples had the lowest abundance of pathogen indicators, suggesting growth-limiting conditions and effective in-dam filtration. Our findings reinforce the value of sealed, sanitary hand pumps for water abstraction from shallow sand aquifers. Ensuring robust construction and regular maintenance of such hand pumps is important for low-income regions relying on shallow groundwater for water with minimal secondary treatment. Potential contamination routes identified at all sites indicate the need for targeted infrastructure improvements and continual maintenance.