Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Type Article
Date 2017-01
Language English
Author(s) Marti Romain1, Ribun Sebastien1, Aubin Jean-Baptiste2, Colinon Celine1, Petit Stephanie1, Marjolet Laurence1, Gourmelon MicheleORCID3, Schmitt Laurent4, Breil Pascal5, Cottet Marylise6, Cournoyer Benoit1
Affiliation(s) 1 : Univ Lyon 1, Res Grp Bacterial Opportunist Pathogens & Environ, Ecol Microbienne INRA1418, UMR CNRS5557,VetAgro Sup, Marcy LEtoile, France.
2 : INSA Lyon, DEEP, Villeurbanne, France.
3 : Inst Francais Rech Exploitat Mer IFREMER, Lab Sante Environm & Microbiol SG2M, RBE Dept, Plouzane, France.
4 : CNRS, ENGEES, LIVE 7362, LTER Zone Atelier Environm Urbaine, Strasbourg, France.
5 : UR HHLY, Inst Natl Rech Sci & Technol Environm & Agr IRSTE, Villeurbanne, France.
6 : Environm Ville Soc, Ecole Normale Super Lyon ENS Lyon Descartes, UMR5600, Lyon, France.
Source Frontiers In Microbiology (1664-302X) (Frontiers Media Sa), 2017-01 , Vol. 8 , N. 19 , P. 1-15
DOI 10.3389/fmicb.2017.00019
WOS© Times Cited 8
Keyword(s) peri-urban river, benthic and hyporheic sediments, microbial community, high throughput sequencing (HTS), fecal contamination
Abstract

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments. OTU patterns were found impacted by combined sewer overflows (CSO) through an observed increase in diversity from the sewer to the hyporheic sediments. These changes appeared driven by direct transfers of bacterial contaminants from wastewaters but also by organic inputs favoring previously undetectable bacterial groups among sediments. These NGS datasets appeared more sensitive at tracking community changes than MST markers. The human-specific MST marker HF183 was strictly detected among CSO-impacted surface waters and not river bed sediments. The ruminant-specific DNA marker was more broadly distributed but intense bovine pollution was required to detect transfers from surface water to benthic and hyporheic sediments. Some OTU showed distribution patterns in line with these MST datasets such as those allocated to the Aeromonas, Acinetobacter, and Pseudomonas. Fecal indicators (Escherichia coli and total thermotolerant coliforms) were detected all over the river course but their concentrations were not correlated with MST ones. Overall, MST and NGS datasets suggested a poor colonization of river sediments by bovine and sewer bacterial contaminants. No environmental outbreak of these bacterial contaminants was detected.

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Table S1 1 144 KB Open access
Table S2 1 26 KB Open access
Table S3 1 91 KB Open access
Table S4 2 92 KB Open access
Table S5 2 139 KB Open access
Table S6 1 86 KB Open access
Table S7 1 21 KB Open access
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Marti Romain, Ribun Sebastien, Aubin Jean-Baptiste, Colinon Celine, Petit Stephanie, Marjolet Laurence, Gourmelon Michele, Schmitt Laurent, Breil Pascal, Cottet Marylise, Cournoyer Benoit (2017). Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses. Frontiers In Microbiology, 8(19), 1-15. Publisher's official version : https://doi.org/10.3389/fmicb.2017.00019 , Open Access version : https://archimer.ifremer.fr/doc/00378/48886/