K. L. Anderson, J. E. Whitlock, and V. J. Harwood, Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments, Appl. Environ. Microbiol, vol.71, pp.3041-3048, 2005.

J. G. Arnold, P. M. Allen, G. Bernhardt, and N. J. ;--s-ashbolt, Microbial contamination of drinking water and disease outcomes in developing regions, J. Hydrol, vol.142, issue.93, pp.229-238, 1993.

R. Bain, R. Cronk, R. Hossain, S. Bonjour, K. Onda et al., Global assessment of exposure to faecal contamination through drinking water based on a systematic review, Trop. Med. Int. Health, vol.19, pp.917-927, 2014.

R. Bain, R. Cronk, J. Wright, H. Yang, T. Slaymaker et al., Fecal contamination of drinking-water in low-and middle-income countries: a systematic review and meta-analysis, PLoS Med, vol.11, p.1001644, 2014.

R. Benner, Chemical composition and reactivity, Biogeochemistry of Marine Dissolved Organic Matter, pp.59-90, 2002.

G. Billen, J. Garnier, and P. Hanset, Modeling phytoplankton development in whole drainage networks -the Riverstrahler model applied to the Seine River system, Hydrobiologia, vol.289, pp.119-137, 1994.

M. Boaretti, M. Del-mar-lleò, B. Bonato, C. Signoretto, and P. Canepari, Involvement of rpoS in the survival of Escherichia coli in the viable but non-culturable state, Environ. Microbiol, vol.5, pp.986-996, 2003.

M. Bouvy, E. Briand, M. M. Boup, P. Got, C. Leboulanger et al., Effects of sewage discharges on microbial components in tropical coastal waters, Mar. Freshw. Res, vol.59, pp.614-626, 2008.

S. B. Brown, C. D. Ikenberry, M. L. Soupir, J. Bisinger, and J. R. Russell, Predicting time cattle spend in streams to quantify direct deposition of manure, Appl. Eng. Agric, vol.30, pp.187-195, 2014.

M. Burmolle, A. Kjoller, and S. J. Sorensen, An invisible workforce: biofilms in the soil, Microbial Biofilm: Current Research and Applications, pp.61-71, 2012.

D. Byamukama, F. Kansiime, R. L. Mach, and A. H. Farnleitner, Determination of Escherichia coli contamination with chromocult coliform agar showed a high level of discrimination efficiency for differing fecal pollution levels in tropical waters of Kampala, Uganda. Appl. Environ. Microbiol, vol.66, pp.864-868, 2000.

D. Byamukama, R. L. Mach, F. Kansiime, M. Manafi, and A. H. Farnleitner, Discrimination efficacy of fecal pollution detection in different aquatic habitats of a high-altitude tropical country, using presumptive coliforms, Escherichia coli, and Clostridium perfringens spores, Appl. Environ. Microbiol, vol.71, pp.65-71, 2005.

M. N. Byappanahalli and R. S. Fujioka, Evidence that tropical soil environment can support the growth of Escherichia coli, Water Sci. Technol, vol.38, pp.171-174, 1998.

M. N. Byappanahalli and R. S. Fujioka, Indigenous soil bacteria and low moisture may limit but allow faecal bacteria to multiply and become a minor population in tropical soils, Water Sci. Technol, vol.50, pp.27-32, 2004.

M. N. Byappanahalli, M. B. Nevers, A. Korajkic, Z. R. Staley, and V. J. Harwood, Enterococci in the environment. Microbiol, Mol. Biol. Rev, vol.76, pp.685-706, 2012.

M. N. Byappanahalli, T. Yan, M. J. Hamilton, S. Ishii, R. S. Fujioka et al., The population structure of Escherichia coli isolated from subtropical and temperate soils, Sci. Total Environ, vol.417, pp.273-279, 2012.

M. N. Byappanahalli, D. A. Shively, M. B. Nevers, M. J. Sadowsky, and R. L. Whitman, Growth and survival of Escherichia coli and enterococci populations in the macro-alga Cladophora (Chlorophyta), FEMS Microbiol. Ecol, vol.46, pp.203-211, 2003.

M. N. Byappanahalli, R. L. Whitman, D. A. Shively, M. J. Sadowsky, and S. Ishii, Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed, Environ. Microbiol, vol.8, pp.504-513, 2006.

M. Carillo, E. Estrada, and T. C. Hazen, Survival and enumeration of the fecal indicators Bifidobacterium adolescentis and Escherichia coli in a tropical rain forest watershed, Appl. Environ. Microbiol, vol.50, pp.468-476, 1985.

N. Chahinian, C. Bancon-montigny, A. Caro, P. Got, J. L. Perrin et al., The role of river sediments in contamination storage downstream of a waste water treatment plant in low flow conditions: organotins, faecal indicator bacteria and nutrients, Estuar. Coast. Shelf. Sci, vol.114, pp.70-81, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01903330

Y. M. Chan, W. Thoe, and J. H. Lee, Field and laboratory studies of Escherichia coli decay rate in subtropical coastal water, J. Hydro Environ. Res, vol.9, pp.1-14, 2015.

K. H. Cho, S. M. Cha, J. Kang, S. W. Lee, Y. Park et al., Meteorological effects on the levels of fecal indicator bacteria in an urban stream: a modeling approach, Water Res, vol.44, pp.2189-2202, 2010.

K. H. Cho, Y. A. Pachepsky, J. H. Kim, A. K. Guber, D. R. Shelton et al., Release of Escherichia coli from the bottom sediment in a first-order creek: experiment and reach-specific modeling, J. Hydrol, vol.391, pp.322-332, 2010.

K. H. Cho, Y. A. Pachepsky, J. H. Kim, J. W. Kim, and M. H. Park, The modified SWAT model for predicting fecal coliforms in the Wachusett Reservoir Watershed, USA, Water Res, vol.46, pp.4750-4760, 2012.

E. Christenson, R. Bain, J. Wright, S. Aondoakaa, R. Hossain et al., Examining the influence of urban definition when assessing relative safety of drinking-water in Nigeria, Sci. Total Environ, vol.490, pp.301-312, 2014.

Y. Chu, C. Salles, M. G. Tournoud, P. Got, M. Troussellier et al., Faecal bacterial loads during flood events in Northwestern Mediterranean coastal rivers, J. Hydrol, vol.405, pp.501-511, 2011.

R. Colwell, Bacterial death revisited, pp.325-342, 2000.

P. Conan, F. Joux, J. P. Torreton, M. Pujo-pay, T. Douki et al., Effect of solar ultraviolet radiation on bacterio-and phytoplankton activity in a large coral reef lagoon (southwest New Caledonia), Aquat. Microb. Ecol, vol.52, pp.83-98, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02054548

J. Crowther, M. D. Wyer, M. Bradford, D. Kay, and C. A. Francis, Modelling faecal indicator concentrations in large rural catchments using land use and topographic data, J. Appl. Microbiol, vol.94, pp.962-973, 2003.

B. C. Crump, J. A. Baross, and C. A. Simenstad, Dominance of particleattached bacteria in the Columbia River estuary, USA, Aquat. Microb. Ecol, vol.14, pp.7-18, 1998.

A. De-brauwere, O. Gourgue, B. De-brye, P. Servais, N. K. Ouattara et al., Integrated modelling of faecal contamination in a densely populated river-sea continuum (Scheldt River and Estuary), Sci. Total Environ, vol.468, pp.31-45, 2014.

R. De-wit and T. Bouvier, Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?, Environ. Microbiol, vol.8, pp.755-758, 2006.

B. J. Dutka and K. K. Kwan, Bacterial die-off and stream transport studies, Water Res, vol.14, pp.909-915, 1980.

E. Ekklesia, P. Shanahan, L. H. Chua, and H. S. Eikaas, Associations of chemical tracers and faecal indicator bacteria in a tropical urban catchment, Water Res, vol.75, pp.270-281, 2015.

E. Ekklesia, P. Shanahan, L. H. Chua, and H. S. Eikaas, Temporal variation of faecal indicator bacteria in tropical urban storm drains, Water Res, vol.68, pp.171-181, 2015.

D. Ferguson and C. Signoretto, Environmental persistence and naturalization of fecal indicator organisms, Microbial Source Tracking: Methods, Applications, and Case Studies, pp.379-397, 2011.

N. Fierer, J. , and R. B. , The diversity and biogeography of soil bacterial communities, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.626-631, 2006.

R. Fujioka and M. Byappanahalli, Microbial ecology controls the establishment of fecal bacteria in tropical soil environment, Advances in Water and Wastewater Treatment Technology: Molecular Technology, pp.273-283, 2001.

V. P. Gannon, G. D. Duke, J. E. Thomas, J. Vanleeuwen, J. Byrne et al., Use of in-stream reservoirs to reduce bacterial contamination of rural watersheds, Sci. Total Environ, vol.348, pp.19-31, 2005.

A. Garzio-hadzick, D. R. Shelton, R. L. Hill, Y. A. Pachepsky, A. K. Guber et al., Survival of manure-borne E. coil in streambed sediment: effects of temperature and sediment properties, Water Res, vol.44, pp.2753-2762, 2010.

E. Gourdin, O. Evrard, S. Huon, I. Lefèvre, O. Ribolzi et al., Suspended sediment dynamics in a Southeast Asian mountainous catchment: combining river monitoring and fallout radionuclide tracers, J. Hydrol, vol.519, pp.1811-1823, 2014.
URL : https://hal.archives-ouvertes.fr/cea-02610607

E. Gourdin, S. Huon, O. Evrard, O. Ribolzi, T. Bariac et al., Sources and export of particle-borne organic matter during a monsoon flood in a catchment of northern Laos, Biogeosciences, vol.12, pp.1073-1089, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01207390

M. Gourmelon, M. P. Caprais, S. Mieszkin, R. Marti, N. Wery et al., Development of microbial and chemical MST tools to identify the origin of the faecal pollution in bathing and shellfish harvesting waters in France, Water Res, vol.44, pp.4812-4824, 2010.
URL : https://hal.archives-ouvertes.fr/insu-00604989

J. Gross, The severe impact of climate change on developing countries, Med. Glob. Surviv, vol.7, pp.96-100, 2002.

V. Guernier, M. E. Hochberg, and J. F. Guegan, Ecology drives the worldwide distribution of human diseases, PLoS Biol, vol.2, p.186, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02393044

V. J. Harwood, C. Staley, B. D. Badgley, K. Borges, and A. Korajkic, Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes, FEMS Microbiol. Rev, vol.38, pp.1-40, 2014.

N. Hofstra, Quantifying the impact of climate change on enteric waterborne pathogen concentrations in surface water, Curr. Opin. Environ. Sustain, vol.3, pp.471-479, 2011.

T. Hrdinka, O. Novický, E. Hanslík, and M. Rieder, Possible impacts of floods and droughts on water quality, J. Hydro Environ. Res, vol.6, pp.145-150, 2012.

S. Ishii, W. B. Ksoll, R. E. Hicks, and M. J. Sadowsky, Presence and growth of naturalized Escherichia coli in temperate soils from lake superior watersheds, Appl. Environ. Microbiol, vol.72, pp.612-621, 2006.

S. Ishii and M. J. Sadowsky, Escherichia coli in the environment: implications for water quality and human health, Microbes Environ, vol.23, pp.101-108, 2008.

K. O. Isobe, M. Tarao, N. H. Chiem, L. Y. Minh, and H. Takada, Effect of environmental factors on the relationship between concentrations of coprostanol and fecal indicator bacteria in tropical (Mekong delta) and temperate (Tokyo) freshwaters, Appl. Environ. Microbiol, vol.70, pp.814-821, 2004.

K. O. Isobe, M. Tarao, M. P. Zakaria, N. H. Chiem, L. Y. Minh et al., Quantitative application of fecal sterols using gas chromatographymass spectrometry to investigate fecal pollution in tropical waters: Western Malaysia and Mekong Delta, Environ. Sci. Technol, vol.36, pp.4497-4507, 2002.

A. Jaffrezic, E. Jarde, A. M. Pourcher, M. Gourmelon, M. P. Caprais et al., Microbial and chemical markers: runoff transfer in animal manure-amended soils, J. Environ. Qual, vol.40, pp.959-968, 2011.
URL : https://hal.archives-ouvertes.fr/insu-00611363

J. S. Jagai, D. A. Castronovo, J. Monchak, and E. N. Naumova, Seasonality of cryptosporidiosis: a meta-analysis approach, Environ. Res, vol.109, pp.465-478, 2009.

J. L. Janeau, L. C. Gillard, S. Grellier, P. Jouquet, T. P. Le et al., Soil erosion, dissolved organic carbon and nutrient losses under different land use systems in a small catchment in northern Vietnam, Agric. Water Manage, vol.146, pp.314-323, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01333633

E. Jarde, G. Gruau, and L. Mansuy-huault, The coprostanol/sterol ratio as indicator of organic matter provenance in soils and rivers, Geochim. Cosmochim. Acta, vol.69, pp.756-756, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00112679

E. Jarde, G. Gruau, and L. Mansuy-huault, Detection of manurederived organic compounds in rivers draining agricultural areas of intensive manure spreading, Appl. Geochem, vol.22, pp.1814-1824, 2007.
URL : https://hal.archives-ouvertes.fr/insu-00165424

L. Jeanneau, E. Jarde, and G. Gruau, Influence of salinity and natural organic matter on the solid phase extraction of sterols and stanols: application to the determination of the human sterol fingerprint in aqueous matrices, J. Chromatogr. A, vol.1218, pp.2513-2520, 2011.
URL : https://hal.archives-ouvertes.fr/insu-00611602

L. Jeanneau, O. Solecki, N. Wery, E. Jardé, M. Gourmelon et al., Relative decay of fecal indicator bacteria and humanassociated markers: a microcosm study simulating wastewater input into seawater and freshwater, Environ. Sci. Technol, vol.46, pp.2375-2382, 2012.
URL : https://hal.archives-ouvertes.fr/insu-00679278

L. Jiminez, I. Muniz, G. A. Toranzos, and T. C. Hazen, Survival and activity of Salmonella typhimurium and Escherichia coli in tropical freshwater, J. Appl. Bacteriol, vol.67, pp.61-69, 1989.

A. Kaisermann, A. Roguet, N. Nunan, P. Maron, N. Ostle et al., Agricultural management affects the response of soil bacterial community structure and respiration to water-stress, Soil Biol. Biochem, vol.66, pp.69-77, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02652776

P. Karanis, C. Kourenti, and H. Smith, Waterborne transmission of protozoan parasites: a worldwide review of outbreaks and lessons learnt, J. Water Health, vol.5, pp.1-38, 2007.

M. R. Karim, F. D. Manshadi, M. M. Karpiscak, and C. P. Gerba, The persistence and removal of enteric pathogens in constructed wetlands, Water Res, vol.38, pp.1831-1837, 2004.

S. M. Kashefipour, B. Lin, E. Harris, and R. A. Falconer, Hydroenvironmental modelling for bathing water compliance of an estuarine basin, Water Res, vol.36, pp.1854-1868, 2002.

J. W. Kim, Y. A. Pachepsky, D. R. Shelton, and C. Coppock, Effect of streambed bacteria release on E. coli concentrations: monitoring and modeling with the modified SWAT, Ecol. Modell, vol.221, pp.1592-1604, 2010.

E. Kimani-murage and A. Ngindu, Quality of water the slum dwellers use: the case of a Kenyan slum, J. Urban Health, vol.84, pp.829-838, 2007.

J. Klaus and J. Mcdonnell, Hydrograph separation using stable isotopes: review and evaluation, J. Hydrol, vol.505, pp.47-64, 2013.

R. W. Kloot, Locating Escherichia coli contamination in a rural South Carolina watershed, J. Environ. Manage, vol.83, pp.402-408, 2007.

A. Korajkic, B. R. Mcminn, V. J. Harwood, O. C. Shanks, G. S. Fout et al., Differential decay of enterococci and Escherichia coli originating from two fecal pollution sources, Appl. Environ. Microbiol, vol.79, pp.2488-2492, 2013.

A. Korajkic, P. Wanjugi, and V. J. Harwood, Indigenous microbiota and habitat influence Escherichia coli survival more than sunlight in simulated aquatic environments, Appl. Environ. Microbiol, vol.79, pp.5329-5337, 2013.

A. Korajkic, B. R. Mcminn, O. C. Shanks, M. Sivaganesan, G. S. Fout et al., Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the upper Mississippi river, Appl. Environ. Microbiol, vol.80, pp.3952-3961, 2014.

W. B. Ksoll, S. Ishii, M. J. Sadowsky, and R. E. Hicks, Presence and sources of fecal coliform bacteria in epilithic periphyton communities of lake superior, Appl. Environ. Microbiol, vol.73, pp.3771-3778, 2007.

O. Kunii, S. Nakamura, R. Abdur, and S. Wakai, The impact on health and risk factors of the diarrhoea epidemics in the 1998 Bangladesh floods, Public Health, vol.116, pp.68-74, 2002.

R. Lal, Soil erosion in the humid tropics with particular reference to agricultural land development and soil management, Proceeding of Symposium on the Hydrology of Humid Tropical Regions with Particular Reference to the Hydrological Effects of Agriculture and Forestry Practice, pp.221-240, 1983.

T. P. Le, G. Billen, J. Garnier, S. Thery, C. Fezard et al., Nutrient (N, P) budgets for the Red River basin (Vietnam and China), Global Biogeochem. Cycles, vol.19, p.2022, 2005.

K. Y. Lee, T. R. Fisher, R. , and E. , Modeling the hydrochemistry of the Choptank river basin using GWLF and Arc/Info: 2. Model validation and application, Biogeochemistry, vol.56, pp.311-348, 2001.

R. Lemee, E. Rochelle-newall, F. Van-wambeke, M. D. Pizay, P. Rinaldi et al., Seasonal variation of bacterial production, respiration and growth efficiency in the open NW Mediterranean Sea, Aquat. Microb. Ecol, vol.29, pp.227-237, 2002.
URL : https://hal.archives-ouvertes.fr/hal-01780314

Z. Liang, Z. He, X. Zhou, C. A. Powell, Y. Yang et al., Impact of mixed land-use practices on the microbial water quality in a subtropical coastal watershed, Sci. Total Environ, vol.449, pp.426-433, 2013.

T. N. Luu, J. Garnier, G. Billen, D. Orange, J. Nemery et al., Hydrological regime and water budget of the Red River Delta (Northern Vietnam), J. Asian Earth Sci, vol.37, pp.219-228, 2010.
URL : https://hal.archives-ouvertes.fr/insu-00563990

F. Magdoff and R. R. Weil, Soil organic matter management strategies, Soil Organic Matter in Sustainable Agriculture, pp.45-66, 2004.

J. Mahloch, Comparative analysis of modeling techniques for coliform organisms in streams, Appl. Microbiol, vol.27, pp.340-345, 1974.

R. L. Mcdaniel, M. L. Soupir, R. B. Tuttle, and A. E. Cervantes, , 2013.

, Release, dispersion, and resuspension of Escherichia coli from direct fecal deposits under controlled flows, J. Am. Water Resour. Assoc, vol.49, pp.319-327

P. Menon, G. Billen, and P. Servais, Mortality rates of autochthonous and fecal bacteria in natural aquatic ecosystems, Water Res, vol.37, pp.4151-4158, 2003.

S. Mieszkin, J. Furet, G. Corthier, and M. Gourmelon, 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.

C. T. Miller, C. N. Dawson, M. W. Farthing, T. Y. Hou, J. Huang et al., Numerical simulation of water resources problems: models, methods, and trends, Adv. Water Resour, vol.51, pp.405-437, 2013.

J. D. Milliman, Sediment discharge to the ocean from small mountainous rivers: the New Guinea example, Geo Mar. Lett, vol.15, pp.127-133, 1995.

J. D. Milliman and R. H. Meade, World-wide delivery of river sediment to the oceans, J. Geol, vol.91, pp.1-21, 1983.

J. D. Milliman and J. P. Syvitski, Geomorphic tectonic control of sediment discharge into the ocean: the importance of small mountainous rivers, J. Geol, vol.100, pp.525-544, 1992.

A. A. Mitch, K. C. Gasner, M. , and W. A. , Fecal coliform accumulation within a river subject to seasonally-disinfected wastewater discharges, Water Res, vol.44, pp.4776-4782, 2010.

R. M. Monaghan, P. L. Carey, R. J. Wilcock, J. J. Drewry, D. J. Houlbrooke et al., Linkages between land management activities and stream water quality in a border dyke-irrigated pastoral catchment, Agric. Ecosyst. Environ, vol.129, pp.201-211, 2009.

O. Navratil, C. Legout, D. Gateuille, M. Esteves, and F. Liebault, Assessment of intermediate fine sediment storage in a braided river reach (southern French Prealps), Hydrol. Process, vol.24, pp.1318-1332, 2010.
URL : https://hal.archives-ouvertes.fr/insu-00564669

M. Neave, H. Luter, A. Padovan, S. Townsend, X. Schobben et al., Multiple approaches to microbial source tracking in tropical northern Australia, vol.3, pp.860-874, 2014.

G. Nichols, C. Lane, N. Asgari, N. Q. Verlander, and A. Charlett, Rainfall and outbreaks of drinking water related disease and in England and Wales, J. Water Health, vol.7, pp.1-8, 2009.

J. P. Nshimyimana, E. Ekklesia, P. Shanahan, L. H. Chua, and J. R. Thompson, Distribution and abundance of human-specific Bacteroides and relation to traditional indicators in an urban tropical catchment, J. Appl. Microbiol, vol.116, pp.1369-1383, 2014.

D. M. Oliver, C. D. Clegg, A. L. Heathwaite, and P. M. Haygarth, Preferential attachment of Escherichia coli to different particle size fractions of an agricultural grassland soil, Water Air Soil Pollut, vol.185, pp.369-375, 2007.

D. M. Oliver, P. M. Haygarth, C. D. Clegg, and L. Heathwaite, Differential E. coli die-off patterns associated with agricultural matrices, Environ. Sci. Technol, vol.40, pp.5710-5716, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02403760

S. Opisa, M. R. Odiere, W. G. Jura, M. S. Diana, D. M. Karanja et al., Faecal contamination of public water sources in informal settlements of Kisumu City, western Kenya, Water Sci. Technol, vol.66, pp.2674-2681, 2012.

K. Otto, H. Elwing, and M. Hermansson, Effect of ionic strength on initial interactions of Escherichia coli with surfaces, studied on-line by a novel quartz crystal microbalance technique, J. Bacteriol, vol.181, pp.5210-5218, 1999.

Y. A. Pachepsky, A. M. Sadeghi, S. A. Bradford, D. R. Shelton, A. K. Guber et al., Transport and fate of manure-borne pathogens: modeling perspective, Agric. Water Manage, vol.86, pp.81-92, 2006.

Y. A. Pachepsky and D. R. Shelton, Escherichia coli and Fecal Coliforms in freshwater and estuarine Sediments, Crit. Rev. Environ. Sci. Technol, vol.41, pp.1067-1110, 2011.

Y. Pachepsky, D. R. Shelton, J. E. Mclain, J. Patel, and R. E. Mandrell, Irrigation waters as a source of pathogenic microorganisms in produce: a review, Advances in Agronomy, pp.73-141, 2011.

P. K. Pandey and M. L. Soupir, Assessing the impacts of E.coli laden streambed sediment on E.coli loads over a range of flows and sediment characteristics, J. Am. Water Resour. Assoc, vol.49, pp.1261-1269, 2013.

P. K. Pandey, M. L. Soupir, M. Haddad, and J. J. Rothwell, Assessing the impacts of watershed indexes and precipitation on spatial in-stream E. coli concentrations, Ecol. Indic, vol.23, pp.641-652, 2012.

P. K. Pandey, M. L. Soupir, and C. R. Rehmann, A model for predicting resuspension of Escherichia coil from streambed sediments, Water Res, vol.46, pp.115-126, 2012.

P. K. Pandey, M. L. Soupir, and C. Ikenberry, Modelling animal waste pathogen transport from agricultural land to streams, Proceedings of the International Conferences on Geological, Geographical, Aerospace and Earth Sciences, 2014.

J. Patin, E. Mouche, O. Ribolzi, V. Chaplot, O. Sengtahevanghoung et al., Analysis of runoff production at the plot scale during a longterm survey of a small agricultural catchment in Lao PDR, J. Hydrol, vol.426, pp.79-92, 2012.

O. Planchon, P. Cadet, J. M. Lapetite, N. Silvera, and M. Esteves, Relationship between raindrop erosion and runoff erosion under simulated rainfall in the Sudano-Sahel: consequences for the spread of nematodes by runoff, Earth Surf. Process Land, vol.25, pp.729-741, 2000.

P. Podwojewski, D. Orange, P. Jouquet, C. Valentin, V. T. Nguyen et al., Land-use impacts on surface runoff and soil detachment within agricultural sloping lands in Northern Vietnam, Catena, vol.74, pp.109-118, 2008.
URL : https://hal.archives-ouvertes.fr/bioemco-00395586

T. Pommier, B. Canback, L. Riemann, K. H. Bostrom, K. Simu et al., Global patterns of diversity and community structure in marine bacterioplankton, Mol. Ecol, vol.16, pp.867-880, 2007.

T. Pommier, A. Merroune, Y. Bettarel, P. Got, J. Janeau et al., Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential, FEMS Microbiol. Ecol, vol.90, pp.622-632, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02487470

M. Ratajczak, E. Laroche, T. Berthe, O. Clermont, B. Pawlak et al., Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed, BMC Microbiol, vol.10, p.222, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00663723

V. R. Regina, A. R. Lokanathan, J. J. Modrzy?ski, D. S. Sutherland, and R. L. Meyer, Surface phsicochemistry and ionic strength affects eDNA's role in bacterial adhesion to abiotic surfaces, PLoS ONE, vol.9, p.105033, 2014.

O. Ribolzi, J. Cuny, P. Sengsoulichanh, C. Mousques, B. Soulileuth et al., Land use and water quality along a mekong tributary in Northern Lao PDR, Environ. Manage, vol.47, pp.291-302, 2011.
URL : https://hal.archives-ouvertes.fr/bioemco-00580394

O. Ribolzi, J. Patin, L. M. Bresson, K. O. Latsachack, E. Mouche et al., Impact of slope gradient on soil surface features and infiltration on steep slopes in northern Laos, Geomorphology, vol.127, pp.53-63, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000473

S. C. Rivera, T. C. Hazen, and G. A. Toranzos, Isolation of fecal coliforms from pristine sites in a tropical rain forest, Appl. Environ. Microbiol, vol.54, pp.513-517, 1988.

E. Rochelle-newall, F. D. Hulot, J. L. Janeau, and A. Merroune, CDOM fluorescence as a proxy of DOC concentration in natural waters: a comparison of four contrasting tropical systems, Environ. Monit. Assess, vol.186, pp.589-596, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02633861

S. M. September, F. A. Els, S. N. Venter, and V. S. Brözel, Prevalence of bacterial pathogens in biofilms of drinking water distribution systems, J. Water Health, vol.5, pp.219-227, 2007.

A. Sinclair, D. Hebb, R. Jamieson, R. Gordon, K. Benedict et al., Growing season surface water loading of fecal indicator organisms within a rural watershed, Water Res, vol.43, pp.1199-1206, 2009.

L. W. Sinton, C. H. Hall, P. A. Lynch, and R. J. Davies-colley, Sunlight inactivation of fecal indicator bacteria and bacteriophages from waste stabilization pond effluent in fresh and saline waters, Appl. Environ. Microbiol, vol.68, pp.1122-1131, 2002.

C. D. Smith, S. G. Berk, M. T. Brandl, and L. W. Riley, Survival characteristics of diarrheagenic Escherichia coli pathotypes and Helicobacter pylori during passage through the free-living ciliate, Tetrahymena sp, FEMS Microbiol. Ecol, vol.82, pp.574-583, 2012.

O. Solecki, L. Jeanneau, E. Jarde, M. Gourmelon, C. Marin et al., Persistence of microbial and chemical pig manure markers as compared to faecal indicator bacteria survival in freshwater and seawater microcosms, Water Res, vol.45, pp.4623-4633, 2011.
URL : https://hal.archives-ouvertes.fr/insu-00622992

H. M. Solo-gabriele, M. A. Wolfert, T. R. Desmarais, and C. J. Palmer, Sources of Escherichia coli in a coastal subtropical environment, Appl. Environ. Microbiol, vol.66, pp.230-237, 2000.

M. L. Soupir and S. Mostaghimi, Escherichia coli and Enterococci attachment to particles in runoff from highly and sparsely vegetated grassland, Water Air Soil Pollut, vol.216, pp.167-178, 2011.

Z. R. Staley, J. R. Rohr, and V. J. Harwood, Test of direct and indirect effects of agrochemicals on the survival of fecal indicator bacteria, Appl. Environ. Microbiol, vol.77, pp.8765-8774, 2011.

Z. R. Staley, J. R. Rohr, J. K. Senkbeil, and V. J. Harwood, Agrochemicals indirectly increase survival of E. coli O157:H7 and indicator bacteria by reducing ecosystem services, Ecol. Appl, vol.24, pp.1945-1953, 2014.

Z. R. Staley, J. K. Senkbeil, J. R. Rohr, and V. J. Harwood, Lack of direct effects of agrochemicals on zoonotic pathogens and fecal indicator bacteria, Appl. Environ. Microbiol, vol.78, pp.8146-8150, 2012.

A. M. Strauch, R. A. Mackenzie, G. L. Bruland, R. Tingley, and C. P. Giardina, Climate change and land use drivers of fecal bacteria in tropical Hawaiian rivers, J. Environ. Qual, vol.43, pp.1475-1483, 2014.

C. H. Stumpf, M. F. Piehler, S. Thompson, and R. T. Noble, Loading of fecal indicator bacteria in North Carolina tidal creek headwaters: hydrographic patterns and terrestrial runoff relationships, Water Res, vol.44, pp.4704-4715, 2010.

E. Suter, A. Juhl, O. 'mullan, and G. , Particle association of Enterococcus and total Bacteria in the Lower Hudson River Estuary, USA. J. Water Resour. Prot, vol.3, pp.715-725, 2011.

W. Thoe, S. H. Wong, K. W. Choi, and J. H. Lee, Daily prediction of marine beach water quality in Hong Kong, J. Hydro Environ. Res, vol.6, pp.164-180, 2012.

W. Thothong, S. Huon, J. L. Janeau, A. Boonsaner, A. De-rouw et al., Impact of land use change and rainfall on sediment and carbon accumulation in a water reservoir of North Thailand, Agric. Ecosyst. Environ, vol.140, pp.521-533, 2011.
URL : https://hal.archives-ouvertes.fr/bioemco-00580382

E. Topp, M. Welsh, Y. C. Tien, A. Dang, G. Lazarovits et al., Strain-dependent variability in growth and survival of Escherichia coli in agricultural soil, FEMS Microbiol. Ecol, vol.44, issue.03, pp.55-57, 2003.

D. Trevisan, J. Y. Vansteelant, and J. M. Dorioz, Survival and leaching of fecal bacteria after slurry spreading on mountain hay meadows: consequences for the management of water contamination risk, Water Res, vol.36, pp.275-283, 2002.

M. Troussellier, P. Got, M. Bouvy, M. Boup, R. Arfi et al., Water quality and health status of the Senegal River estuary, Mar. Pollut. Bull, vol.48, pp.852-862, 2004.

P. Vidon, M. A. Campbell, and M. Gray, Unrestricted cattle access to streams and water quality in till landscape of the Midwest, Agric. Water Manage, vol.95, pp.322-330, 2008.

P. Vidon, L. P. Tedesco, J. Wilson, M. A. Campbell, L. R. Casey et al., Direct and indirect hydrological controls on E. coli concentration and loading in Midwestern streams, J. Environ. Qual, vol.37, pp.1761-1768, 2008.

O. Vigiak, O. Ribolzi, A. Pierret, O. Sengtaheuanghoung, and C. Valentin, Trapping efficiencies of cultivated and natural riparian vegetation of northern Laos, J. Environ. Qual, vol.37, pp.889-897, 2008.
URL : https://hal.archives-ouvertes.fr/bioemco-00395583

K. Vijayavel, M. J. Sadowsky, J. A. Ferguson, and D. R. Kashian, The establishment of the nuisance cyanobacteria Lyngbya wollei in Lake St. Clair and its potential to harbor fecal indicator bacteria, J. Great Lakes Res, vol.39, pp.560-568, 2013.

P. Wanjugi and V. J. Harwood, The influence of predation and competition on the survival of commensal and pathogenic fecal bacteria in aquatic habitats, Environ. Microbiol, vol.15, pp.517-526, 2013.

J. Wanyama, K. Herremans, W. Maetens, M. Isabirye, F. Kahimba et al., Effectiveness of tropical grass species as sediment filters in the riparian zone of Lake Victoria. Soil Use Manage, vol.28, pp.409-418, 2012.

J. Wilkinson, A. Jenkins, M. Wyer, K. , and D. , Modelling faecal coliform dynamics in streams and rivers, Water Res, vol.29, issue.94, p.211, 1995.

M. D. Winfield and E. A. Groisman, Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli, Appl. Environ. Microbiol, vol.69, pp.3687-3694, 2003.

J. Wingender and H. Flemming, Biofilms in drinking water and their role as reservoir for pathogens, Int. J. Hyg. Environ. Health, vol.214, pp.417-423, 2011.

A. Yajima and H. Kurokura, Microbial risk assessment of livestockintegrated aquaculture and fish handling in Vietnam, Fish. Sci, vol.74, pp.1062-1068, 2008.

W. W. Zhang, H. Li, D. F. Sun, and L. D. Zhou, A statistical assessment of the impact of agricultural land use intensity on regional surface water quality at multiple scales, Int. J. Environ. Res. Public Health, vol.9, pp.4170-4186, 2012.

A. D. Ziegler, J. Negishi, R. C. Sidle, P. Preechapanya, R. A. Sutherland et al., Reduction of stream sediment concentration by a riparian buffer: filtering of road runoff in disturbed headwater basins of montane mainland southeast Asia, J. Environ. Qual, vol.35, pp.151-162, 2006.

A. Zita and M. Hermansson, Effects of ionic strength on bacterial adhesion and stability of flocs in a wastewater activated sludge system, Appl. Environ. Microbiol, vol.60, pp.3041-3048, 1994.

E. G. Zoetendal, J. Raes, . Van-den, B. Bogert, M. Arumugam et al., The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates, ISME J, vol.6, pp.1415-1426, 2012.