Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters

Esther Karunakaran; Rick Battarbee; Simon Tait; Bruno Melo Brentan; Cathal Berney; James Grinham; Maria Angeles Herrero; Ronex Omolo; Isabel Douterelo

doi:10.1016/j.scitotenv.2023.168565

Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters

Sci Total Environ. 2024 Feb 20:912:168565. doi: 10.1016/j.scitotenv.2023.168565. Epub 2023 Nov 17.

Authors

Esther Karunakaran¹, Rick Battarbee², Simon Tait³, Bruno Melo Brentan⁴, Cathal Berney⁵, James Grinham¹, Maria Angeles Herrero³, Ronex Omolo³, Isabel Douterelo⁶

Affiliations

¹ Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK.
² Environmental Change Research Centre, University College London, London WC1E 6BT, UK; Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK.
³ Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK.
⁴ Hydraulic Engineering and Water Resource Department, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil.
⁵ Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK.
⁶ Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK. Electronic address: i.douterelo@sheffield.ac.uk.

PMID: 37979848
DOI: 10.1016/j.scitotenv.2023.168565

Abstract

Rivers are at risk from a variety of pollution sources. Faecal pollution is of particular concern since it disperses pathogenic microorganisms in the aquatic environment. Currently, faecal pollution levels in rivers is monitored using faecal indicator bacteria (FIB) that do not offer information about pollution sources and associated risks. This study used a combined molecular approach, along with measurements of water quality, to gain information on pollution sources, and risk levels, in a newly designated recreational bathing site in the River Wharfe (UK). Physico-chemical parameters were monitored in situ, with water quality multiparameter monitoring sondes installed during the 2021 bathing season. The molecular approach was based on quantitative PCR (qPCR)-aided Microbial Source Tracking (MST) and 16S rRNA gene metabarcoding to obtain a fingerprint of bacterial communities and identify potential bioindicators. The analysis from the water quality sondes showed that ammonium was the main parameter determining the distribution of FIB values. Lower faecal pollution levels were detected in the main river when compared to tributaries, except for samples in the river located downstream of a wastewater treatment plant. The faecal pollution type (anthropogenic vs. zoogenic) changed the diversity and the structure of bacterial communities, giving a distinctive fingerprint that can be used to inform source. DNA-based methods showed that the presence of human-derived bacteria was associated with Escherichia coli spikes, coinciding with higher bacterial diversity and the presence of potential pathogenic bacteria mainly of the genus Mycobacterium, Aeromonas and Clostridium. Samples collected after a heavy rainfall event were associated with an increase in Bacteroidales, which are markers of faecal pollution, including Bacteroides graminisolvens, a ruminant marker associated with surface run-off from agricultural sources. The combined use of qPCR and 16S rRNA sequencing was able to identify pollution sources, and novel bacterial indicators, thereby aiding decision-making and management strategies in recreational bathing rivers.

Keywords: Bacterial communities; Bathing water; Faecal pollution; Microbial source tracking.

MeSH terms

Bacteria / genetics
Environmental Monitoring* / methods
Escherichia coli / genetics
Feces / microbiology
Humans
RNA, Ribosomal, 16S
Water Microbiology*
Water Pollution / analysis
Water Quality

Substances

RNA, Ribosomal, 16S