PMID- 28174557
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20200930
IS  - 1664-302X (Print)
IS  - 1664-302X (Electronic)
IS  - 1664-302X (Linking)
VI  - 8
DP  - 2017
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.
PG  - 19
LID - 10.3389/fmicb.2017.00019 [doi]
LID - 19
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.
FAU - Marti, Romain
AU  - Marti R
AD  - Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR 
      CNRS5557, INRA1418 Ecologie Microbienne, Universite Lyon 1, VetAgro Sup Marcy 
      L'Etoile, France.
FAU - Ribun, Sebastien
AU  - Ribun S
AD  - Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR 
      CNRS5557, INRA1418 Ecologie Microbienne, Universite Lyon 1, VetAgro Sup Marcy 
      L'Etoile, France.
FAU - Aubin, Jean-Baptiste
AU  - Aubin JB
AD  - DEEP, INSA Lyon Villeurbanne, France.
FAU - Colinon, Celine
AU  - Colinon C
AD  - Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR 
      CNRS5557, INRA1418 Ecologie Microbienne, Universite Lyon 1, VetAgro Sup Marcy 
      L'Etoile, France.
FAU - Petit, Stephanie
AU  - Petit S
AD  - Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR 
      CNRS5557, INRA1418 Ecologie Microbienne, Universite Lyon 1, VetAgro Sup Marcy 
      L'Etoile, France.
FAU - Marjolet, Laurence
AU  - Marjolet L
AD  - Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR 
      CNRS5557, INRA1418 Ecologie Microbienne, Universite Lyon 1, VetAgro Sup Marcy 
      L'Etoile, France.
FAU - Gourmelon, Michele
AU  - Gourmelon M
AD  - Institut Francais de Recherche pour l'Exploitation de la Mer (IFREMER), 
      SG2M-Laboratoire Sante Environnement et Microbiologie, RBE Departement Plouzane, 
      France.
FAU - Schmitt, Laurent
AU  - Schmitt L
AD  - LIVE 7362 Centre National de la Recherche Scientifique-ENGEES, LTER - "Zone 
      Atelier Environnementale Urbaine" Strasbourg, France.
FAU - Breil, Pascal
AU  - Breil P
AD  - Institut National de Recherche en Sciences et Technologies pour l'Environnement 
      et l'Agriculture (IRSTEA), UR HHLY Villeurbanne, France.
FAU - Cottet, Marylise
AU  - Cottet M
AD  - UMR5600 "Environnement Ville Societe," Ecole Normale Superieure de Lyon (ENS) 
      Lyon - Descartes Lyon, France.
FAU - Cournoyer, Benoit
AU  - Cournoyer B
AD  - Research Group on "Bacterial Opportunistic Pathogens and Environment", UMR 
      CNRS5557, INRA1418 Ecologie Microbienne, Universite Lyon 1, VetAgro Sup Marcy 
      L'Etoile, France.
LA  - eng
PT  - Journal Article
DEP - 20170124
PL  - Switzerland
TA  - Front Microbiol
JT  - Frontiers in microbiology
JID - 101548977
PMC - PMC5258724
OTO - NOTNLM
OT  - benthic and hyporheic sediments
OT  - fecal contamination
OT  - high throughput sequencing (HTS)
OT  - microbial community
OT  - peri-urban river
EDAT- 2017/02/09 06:00
MHDA- 2017/02/09 06:01
PMCR- 2017/01/24
CRDT- 2017/02/09 06:00
PHST- 2016/09/16 00:00 [received]
PHST- 2017/01/04 00:00 [accepted]
PHST- 2017/02/09 06:00 [entrez]
PHST- 2017/02/09 06:00 [pubmed]
PHST- 2017/02/09 06:01 [medline]
PHST- 2017/01/24 00:00 [pmc-release]
AID - 10.3389/fmicb.2017.00019 [doi]
PST - epublish
SO  - Front Microbiol. 2017 Jan 24;8:19. doi: 10.3389/fmicb.2017.00019. eCollection 
      2017.