Marine sediments are identified as an environmental reservoir for Escherichia coli : Comparing signature-based and novel amplicon sequencing approaches for microbial source tracking
(2024) In Science of the Total Environment 907.- Abstract
Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using... (More)
Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.
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- author
- Frank, Ellinor M. LU ; Ahlinder, Jon ; Jephson, Therese LU ; Persson, Kenneth M. LU ; Lindberg, Elisabet and Paul, Catherine J. LU
- organization
- publishing date
- 2024-01-10
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Amplicon sequencing, Bacterial communities, Escherichia coli, Source tracking, Urban sediments
- in
- Science of the Total Environment
- volume
- 907
- article number
- 167865
- publisher
- Elsevier
- external identifiers
-
- scopus:85174611151
- pmid:37863217
- ISSN
- 0048-9697
- DOI
- 10.1016/j.scitotenv.2023.167865
- language
- English
- LU publication?
- yes
- additional info
- Funding Information: The authors would like to thank the City of Helsingborg and the captains of the boat Sabella for making the sampling of the sediments possible. This project was supported by funding from Vinnova project Urban Magma ( 2015-07054 ); and Sweden Water Research , NSVA and VASYD , and the cities of Helsingborg and Malmö within the Urbana Bad project. Funding Information: The authors would like to thank the City of Helsingborg and the captains of the boat Sabella for making the sampling of the sediments possible. This project was supported by funding from Vinnova project Urban Magma (2015-07054); and Sweden Water Research, NSVA and VASYD, and the cities of Helsingborg and Malmö within the Urbana Bad project. Publisher Copyright: © 2023 The Authors
- id
- 1e71a119-8175-4e8e-953b-84b624a9a607
- date added to LUP
- 2023-11-13 14:04:37
- date last changed
- 2024-06-20 10:31:48
@article{1e71a119-8175-4e8e-953b-84b624a9a607,
abstract = {{<p>Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.</p>}},
author = {{Frank, Ellinor M. and Ahlinder, Jon and Jephson, Therese and Persson, Kenneth M. and Lindberg, Elisabet and Paul, Catherine J.}},
issn = {{0048-9697}},
keywords = {{Amplicon sequencing; Bacterial communities; Escherichia coli; Source tracking; Urban sediments}},
language = {{eng}},
month = {{01}},
publisher = {{Elsevier}},
series = {{Science of the Total Environment}},
title = {{Marine sediments are identified as an environmental reservoir for Escherichia coli : Comparing signature-based and novel amplicon sequencing approaches for microbial source tracking}},
url = {{http://dx.doi.org/10.1016/j.scitotenv.2023.167865}},
doi = {{10.1016/j.scitotenv.2023.167865}},
volume = {{907}},
year = {{2024}},
}