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Application of Next-Generation Sequencing for detection of human and animal faecal pollution in surface waters
Dissertation

Application of Next-Generation Sequencing for detection of human and animal faecal pollution in surface waters

Christian O'Dea
Doctor of Philosophy, University of the Sunshine Coast, Queensland
2026
DOI:
https://doi.org/10.25907/01019
pdf
Thesis2.77 MB
ThesisCC BY-NC V4.0,  Embargoed Access, Embargo ends: 09-Mar-2027

Abstract

Microbiology not elsewhere classified Microbial Source Tracking environmental management public health protection molecular techniques qPCR next-generation sequencing (NGS) water quality freshwater ecosystems
Faecal contamination of surface waters poses ongoing risks to public health and ecosystem integrity, particularly in mixed-use catchments where multiple human and animal sources contribute simultaneously. Traditional water quality monitoring relies on faecal indicator bacteria (FIB), which provide a general indication of contamination but cannot resolve pollution sources. Microbial source tracking (MST) methods have therefore been developed to improve source attribution by targeting host-associated microorganisms, with recent advances in next-generation sequencing (NGS) offering new opportunities for community-based approaches. This thesis comprises four interconnected studies investigating the application of molecular and sequencing-based MST approaches for the detection and characterisation of human and animal faecal pollution in subtropical freshwater catchments. The first study quantified the environmental load of faecal contamination and assessed spatial–temporal variation across contrasting land-use catchments using established MST markers. The second study evaluated the stability and resolution of faecal taxon libraries using computational source attribution modelling to improve discrimination among human, livestock, domestic animal, and wildlife inputs. The third study analysed the gut microbiota of Macropus giganteus using next-generation sequencing to determine the most informative 16S rRNA hypervariable regions for wildlife-associated MST applications. The fourth study developed and validated host-specific molecular markers for detecting human and canine faecal contamination in surface waters. Collectively, this thesis demonstrates how integrating contamination quantification, computational source attribution, wildlife microbiome profiling, and host-specific marker development can improve the resolution and interpretation of faecal pollution sources in complex environmental catchments.

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