Date of Award

Summer 6-1-2026

Document Type

Thesis

Degree Name

Master of Biological Science (MBioSci)

Department

Biology

First Advisor

Samuel Mutiti

Abstract

Groundwater is a critical source of drinking water and urban water security; however, in many developing countries, its exploitation and management are poorly regulated, increasing vulnerability to microbial contamination. Groundwater bacterial communities were characterized using a next-generation sequencing (NGS) metagenomic approach based on long-read 16S rRNA gene (V3–V4 region) amplicon sequencing via Oxford Nanopore Water samples collected from boreholes in planned and unplanned settlements located within carbonate and schist formations were analyzed to profile microbial communities and assess relative microbial risk using the Relative Microbial Risk Index (RMRI). Microbial community composition varied by geology, while unplanned communities exhibited higher pathogen abundance and RMRI values. Across all samples, Pseudomonadota was the dominant phylum, primarily represented by Gammaproteobacteria and Betaproteobacteria, together with Actinomycetota, Bacillota, and Candidatus Brocadia. Species-level analysis identified opportunistic pathogens, including Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica, as well as environmentally persistent taxa such as Dechloromonas sp. A34 and Candidatus Kuenenia stuttgartiensis. Fecal indicator organisms, including Escherichia coli and Enterococcus faecalis, were also detected, suggesting potential fecal contamination. Multivariate analyses indicated that geological setting was strongly associated with microbial community structure, while groundwater from unplanned communities relying on pit latrines exhibited distinct microbial profiles compared to planned communities using septic systems. These findings highlight significant public health risks associated with untreated groundwater and underscore the need for integrated sanitation improvement, routine microbial monitoring, and hydrogeological informed water safety management.

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