Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment

• Published in: Water research (Oxford) 2022-06, Vol.218, p.118534-118534, Article 118534
• Main Authors: Williams, Nathan L.R., Siboni, Nachshon, Potts, Jaimie, Campey, Meredith, Johnson, Colin, Rao, Shivanesh, Bramucci, Anna, Scanes, Peter, Seymour, Justin R.
• Format: Article
• Language: English
• Subjects: Antibiotic resistance genes; Arcobacter; Microbial source tracking; qPCR, 16S rRNA gene amplicon sequencing; Water quality
• ISSN: 0043-1354; 1879-2448
• DOI: 10.1016/j.watres.2022.118534

•Molecular MST methods identify faecal pollution cause (human and dog faeces).•Molecular MST methods identify faecal pollution source location at urban beach.•Microbial hazards including ARGs linked to faecal contamination were identified.•16S data paired with Sourcetracker and indicspecies augmented MST methods. Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from th