Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses.
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 toFlavobacteriumandAquabacterium. Relative numbers ofGaiella, Haliangium, andThermoleophilumOTU 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 theAeromonas, Acinetobacter, andPseudomonas. Fecal indicators (Escherichia coliand 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.
Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup Marcy L'Etoile, France.
Romain
R
Marti
Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup Marcy L'Etoile, France.
Sébastien
S
Ribun
DEEP, INSA Lyon Villeurbanne, France.
Jean-Baptiste
JB
Aubin
Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup Marcy L'Etoile, France.
Céline
C
Colinon
Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup Marcy L'Etoile, France.
Stéphanie
S
Petit
Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup Marcy L'Etoile, France.
Laurence
L
Marjolet
Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), SG2M-Laboratoire Santé Environnement et Microbiologie, RBE Département Plouzané, France.
Michèle
M
Gourmelon
LIVE 7362 Centre National de la Recherche Scientifique-ENGEES, LTER - "Zone Atelier Environnementale Urbaine" Strasbourg, France.
Laurent
L
Schmitt
Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), UR HHLY Villeurbanne, France.
Pascal
P
Breil
UMR5600 "Environnement Ville Société," École Normale Supérieure de Lyon (ENS) Lyon - Descartes Lyon, France.
Marylise
M
Cottet
Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup Marcy L'Etoile, France.
Benoit
B
Cournoyer
benthic and hyporheic sediments; fecal contamination; high throughput sequencing (HTS); microbial community; peri-urban river