FN Archimer Export Format
PT J
TI Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses
BT 
AF MARTI, Romain
   RIBUN, Sebastien
   AUBIN, Jean-Baptiste
   COLINON, Celine
   PETIT, Stephanie
   MARJOLET, Laurence
   GOURMELON, Michele
   SCHMITT, Laurent
   BREIL, Pascal
   COTTET, Marylise
   COURNOYER, Benoit
AS 1:1;2:1;3:2;4:1;5:1;6:1;7:3;8:4;9:5;10:6;11:1;
FF 1:;2:;3:;4:;5:;6:;7:PDG-RBE-SG2M-LSEM;8:;9:;10:;11:;
C1 Univ Lyon 1, Res Grp Bacterial Opportunist Pathogens & Environ, Ecol Microbienne INRA1418, UMR CNRS5557,VetAgro Sup, Marcy LEtoile, France.
   INSA Lyon, DEEP, Villeurbanne, France.
   Inst Francais Rech Exploitat Mer IFREMER, Lab Sante Environm & Microbiol SG2M, RBE Dept, Plouzane, France.
   CNRS, ENGEES, LIVE 7362, LTER Zone Atelier Environm Urbaine, Strasbourg, France.
   UR HHLY, Inst Natl Rech Sci & Technol Environm & Agr IRSTE, Villeurbanne, France.
   Environm Ville Soc, Ecole Normale Super Lyon ENS Lyon Descartes, UMR5600, Lyon, France.
C2 UNIV LYON, FRANCE
   INSA LYON, FRANCE
   IFREMER, FRANCE
   CNRS, FRANCE
   IRSTEA, FRANCE
   ENS LYON, FRANCE
SI BREST
SE PDG-RBE-SG2M-LSEM
IN WOS Ifremer jusqu'en 2018
   DOAJ
   copubli-france
   copubli-p187
   copubli-univ-france
IF 4.019
TC 16
UR https://archimer.ifremer.fr/doc/00378/48886/49316.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49317.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49318.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49319.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49320.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49321.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49322.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49323.pdf
   https://archimer.ifremer.fr/doc/00378/48886/49324.tif
   https://archimer.ifremer.fr/doc/00378/48886/49325.tif
   https://archimer.ifremer.fr/doc/00378/48886/49326.tif
LA English
DT Article
DE ;peri-urban river;benthic and hyporheic sediments;microbial community;high throughput sequencing (HTS);fecal contamination
AB 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. 
PY 2017
PD JAN
SO Frontiers In Microbiology
SN 1664-302X
PU Frontiers Media Sa
VL 8
IS 19
UT 000412799300001
BP 1
EP 15
DI 10.3389/fmicb.2017.00019
ID 48886
ER

EF