Suitability of bacterial and viral markers for faecal source tracking in the coastal environment

Aims The accurate identification of faecal contamination sources in coastal environments is critical for public health protection and effective water quality management. This study evaluated the suitability of a range of bacterial and viral molecular markers for microbial source tracking (MST) in treated and untreated urban wastewater and coastal matrices (water, sediment, and shellfish) along the North Wales coastline. Methods and Results Human-associated markers (crAssphage, BK polyomavirus, adenovirus F, Aichi virus, norovirus, pepper mild mottle virus [PMMoV], and Bacteroides markers pBI143 and HF183) and animal-associated markers (atadenovirus and Catellicoccus marimammalium) were quantified using qPCR and reverse transcription (RT-)qPCR. We also investigated indicator prevalence in the solid vs. liquid phase of wastewater and in water samples concentrated using either ultrafiltration or precipitation. We found that tangential flow ultrafiltration provided superior recovery of the markers compared to skimmed milk precipitation. Results showed that crAssphage, PMMoV, and Bacteroides markers were consistently detected at high concentrations in wastewater and in coastal environmental samples, suggesting they are robust indicators of human faecal contamination. Marker prevalence varied by sample type in the aquatic environment: noroviruses were most abundant in shellfish, while crAssphage dominated in water and sediment. Animal-associated markers were less frequently detected. Conclusions Our findings support the use of crAssphage, PMMoV, and Bacteroides markers for MST and quantitative risk assessment in coastal environments. We recommend matrix-specific marker selection based on pollution sources and sample type, and the use of multiple markers (e.g. viral/bacterial and human/animal-specific) for a holistic assessment.