Persistence of Bacteroides species populations in a river as measured by molecular and culture techniques, Water Quality: Guidelines, Standards and Health, vol.76, pp.7608-7616, 2001. ,
Linking sediment biofilms, hydrodynamics, and River Bed clogging: evidence from a Large River, Microb. Ecol, vol.37, pp.185-196, 1999. ,
Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes, Appl. Environ. Microbiol, vol.66, pp.1587-1594, 2000. ,
A PCR assay To discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA, Appl. Environ. Microbiol, vol.66, pp.4571-4574, 2000. ,
Transport and fate of microbial pathogens in agricultural settings, Crit. Rev. Env. Sci. Technol, vol.43, pp.775-893, 2013. ,
Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed, Water Res, vol.101, pp.498-509, 2016. ,
Fate and transport of pathogens in lakes and reservoirs, Environ. Int, vol.30, pp.741-759, 2004. ,
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments, Clin. Chem, vol.55, pp.611-622, 2009. ,
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, p.421, 2010. ,
Bergey's Manual of Systematic Bacteriology, The Proteobacteria, p.1105, 2005. ,
Microbial respiration within a floodplain aquifer of a large gravel-bed river, Freshw. Biol, vol.47, pp.251-261, 2002. ,
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.14691-14696, 2010. ,
Health Effects Criteria for Fresh Recreational Waters, 1984. ,
Fecal source tracking, the indicator paradigm, and managing water quality, Water Res, vol.41, pp.3517-3538, 2007. ,
Survival and detection of Bacteroides spp., prospective indicator bacteria, Appl. Environ. Microbiol, vol.49, pp.148-150, 1985. ,
Comparison of bacterial production in sediments, epiphyton and the pelagic zone of a lowland river, Freshw. Biol, vol.46, pp.1335-1348, 2001. ,
Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species, Appl. Environ. Microbiol, vol.71, pp.5999-6007, 2005. ,
Quantitative real-time PCR assays for sensitive detection of Canada Goose-Specific fecal pollution in water sources, Appl. Environ. Microbiol, vol.76, pp.4886-4889, 2010. ,
Evaluation of hostspecific Bacteroidales 16S rRNA gene markers as a complementary tool for detecting fecal pollution in a prairie watershed, Water Res, vol.43, pp.4838-4849, 2009. ,
Rainfall-induced runoff from exposed streambed sediments: an important source of water pollution, J. Environ. Qual, vol.44, pp.236-247, 2015. ,
Hydrological exchange and sediment characteristics in a riverbank: relationship between heavy metals and invertebrate community structure, Can. J. Fish. Aquat. Sci, vol.52, pp.2084-2097, 1995. ,
Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and public health protection, Appl. Environ. Microbiol, vol.71, pp.3163-3170, 2005. ,
Aeromonas hydrophila infection in Xenopus laevis, Lab. Anim. Sci, vol.31, pp.297-300, 1981. ,
Spatial and temporal drivers of zoonotic pathogen contamination of an agricultural watershed, J. Environ. Qual, vol.41, pp.242-252, 2012. ,
Microbial contamination detection in water resources: interest of current optical methods, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01122209
, Int. J. Environ. Res. Public Health, vol.11, pp.4292-4310
A conceptual framework for invasion in microbial communities, ISME J, vol.10, pp.2773-2775, 2016. ,
Distribution of microbiological indicators of fecal pollution in the riverine substrates, Environ. Monit. Assess, vol.172, pp.623-630, 2011. ,
Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution, Appl. Environ. Microbiol, vol.61, pp.1171-11790, 1995. ,
Refinement of biomonitoring of urban water courses by combining descriptive and ecohydrological approaches, Ecohydrol. Hydrol, vol.10, pp.3-11, 2009. ,
URL : https://hal.archives-ouvertes.fr/halshs-00660753
, Rapport d'Expertise Collective AFSSET/ANSES. Risques Sanitaires Liés Aux Baignades Artificielles: Évaluation Des Risques Sanitaires, p.180, 2009.
Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing, Ecol. Eng, vol.72, pp.56-66, 2014. ,
River Ecosystem Ecology: A Global Perspective. Encyclooedia of Inland Waters, 2010. ,
Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems, Ecol. Lett, vol.13, pp.1560-1572, 2010. ,
pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing, Front. Microbiol, vol.6, p.285, 2015. ,
Which sequencing depth is sufficient to describe patterns in bacterial ?-and ?-diversity?, Environ. Microbiol. Rep, vol.4, pp.367-372, 2012. ,
Nutrient dynamics in river bed sediments: effects of hydrological disturbances using experimental flow manipulations, J. Soils Sediments, vol.13, pp.207-219, 2013. ,
URL : https://hal.archives-ouvertes.fr/halsde-00786373
Use of pyrosequencing to explore the benthic bacterial community structure in a river impacted by wastewater treatment plant discharges, Res. Microbiol, vol.165, pp.468-471, 2014. ,
Quantitative multi-year elucidation of fecal sources of waterborne pathogen contamination in the South Nation River basin using Bacteroidales microbial source tracking markers, Water Res, vol.47, pp.2315-2324, 2013. ,
Development and validation of a microbial source tracking marker for the detection of fecal pollution by muskrats, J. Microbiol. Methods, vol.87, pp.82-88, 2011. ,
Assessment of a new Bacteroidales marker targeting North American beaver (Castor canadensis) fecal pollution by real-time PCR, J. Microbiol. Methods, vol.95, pp.201-206, 2013. ,
Estimation of pig fecal contamination in a river catchment by real-time PCR using two pigspecific Bacteroidales 16S rRNA genetic markers, Appl. Environ. Microbiol, vol.75, pp.3045-3054, 2009. ,
Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR, J. Appl. Microbiol, vol.108, pp.974-984, 2010. ,
Contribution of the hyporheic zone to ecosystem metabolism in a prealpine gravel-bed river, J. N. Am. Benthol. Soc, vol.16, pp.794-804, 1997. ,
Stream pollution concentration in riffle geomorphic units (Yzeron basin, France), Sci. Total Environ, vol.532, pp.80-90, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01229882
Global patterns in the biogeography of bacterial taxa, Environ. Microbiol, vol.13, pp.135-144, 2011. ,
Vegan: Community Ecology Package. R Package Version 2.2-1, 2015. ,
Characterization of Pseudomonas aeruginosa PB112 (JN996498) isolated from infected Labeo bata (Hamilton) by 16S rRNA gene sequence analysis and fatty acid methyl ester (FAME) analysis, Afr. J. Biotechnol, vol.12, pp.400-405, 2013. ,
, R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing. Available online at, vol.4, pp.307-334, 2015.
Importance of interactions between the water column and the sediment for microbial concentrations in streams, Water Res, vol.43, pp.4579-4589, 2009. ,
Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions, Appl. Environ. Microbiol, vol.72, pp.5610-5614, 2006. ,
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data, Bioinformatics, vol.29, pp.3100-3101, 2013. ,
State of the art molecular markers for fecal pollution source tracking in water, Appl. Microbiol. Biotechnol, vol.89, pp.1341-1355, 2011. ,
Bacterial diversity along a 2600 km river continuum, Environ. Microbiol, vol.17, pp.4994-5007, 2015. ,
Introducing mothur: open-source, platformindependent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol, vol.75, pp.7537-7541, 2009. ,
Denitrification across landscapes and waterscapes: a synthesis, Ecol. Appl, vol.6, pp.2064-2090, 2006. ,
Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater, Environ. Microbiol, vol.7, pp.249-259, 2005. ,
Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake, Water Res, vol.46, pp.5799-5812, 2012. ,
The Aetiology, Histopathology, and ultrastructural features of perianal erythema (Red Anus Syndrome) in the European Eel (Anguilla anguilla), PLoS ONE, vol.9, p.90790, 2014. ,
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, Mol. Biol. Evol, vol.30, pp.2725-2729, 2013. ,
Pathogenecity of Pseudomonas aeruginosa in Oreochromis mossambicus and treatment using lime oil nanoemulsion, Colloids Surf. B. Biointerfaces, vol.116, pp.372-377, 2014. ,
The use of next generation sequencing in the diagnosis and typing of respiratory infections, J. Clin. Virol, vol.69, pp.96-100, 2015. ,
Fate of bacterial production in a heterotrophic ecosystem: Grazing by protists and metazoans in the Hudson Estuary, Mar. Ecol. Prog. Ser, vol.89, pp.155-163, 1992. ,
, USEPA, Microbial Source Tracking Guide, 2005.
Long-term monitoring of waterborne pathogens and microbial source tracking markers in paired-agricultural watersheds under controlled and conventional tile drainage management, Appl. Environ. Microbiol, vol.80, pp.3708-3720, 2014. ,
Coherence among different microbial source tracking markers in a small agricultural stream with and without livestock exclusion practices, Appl. Environ. Microbiol, vol.79, pp.6207-6219, 2013. ,
Associations among pathogenic bacteria, parasites, and environmental and land use factors in multiple mixed-use watersheds, Water Res, vol.45, pp.5807-5825, 2011. ,
, WHO Guidelines for Drinking-Water Quality. Geneva, World Health Organization, 2003.