Seasonal variability of faecal indicator bacteria numbers and die-off rates in the Red River basin, North Viet Nam (Article 1)

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Faecal indicator bacteria

Faecal indicator bacteria

Introduction and definition

Microbiological contamination of water supplies is a globally important problem and poor water quality is a major brake on development. The World Health Organization (WHO) estimates that almost 2 million deaths annually are due to the consumption of contaminated water (WHO, 2012). River water subject to wastewater contamination is often used for washing of clothes and food utensils and for bathing and even cooking (Bain et al., 2014). This is true for urban and peri-urban areas where population densities are high (Ashbolt, 2004; Bain et al., 2014) as well as in rural areas where water supplies are often informal and therefore unregulated. In Asia over 40% of rural drinking water sources are contaminated as compared to only 12% in urban areas. Access to clean water is therefore a problem faced by both urban and rural populations in developing countries.
Considering the known risks associated with the consumption of sewages contaminated water, it is critical to identify the factors that control the persistence and dissemination of these microbial pathogens. By increasing the knowledge based on the dynamics of the water borne pathogens in tropical ecosystems we will be able to reduce the risks associated with the use of untreated water. Moreover, understanding the links between human activities, natural process and biogeochemical functioning and their ultimate impacts on human health are prerequisites for efficient water resources management. However, the data required to adequately understand and interpret these links is often missing or of poor quality in many developing countries (Rochelle-Newall et al., 2015).
Developing countries are faced with a double problem. Often no adequate structures exist for long term monitoring of water borne pathogens in the environment due to economic constraints and secondly, very little knowledge exists on the distribution of these microbes in tropical environments. In order to detect these waterborne pathogens at limited cost, Faecal Indicator Bacteria (FIB) are used as a proxy for pathogenic bacteria. The term FIB describes the range of bacteria that inhabit the gastrointestinal tract of homeothermic animals and includes Escherichia coli and the faecal coliforms, Enterococcus spp., all of which are found in faecal material.
Fecal coliforms (FC) and E.coli (EC) have been used as the standard indicator of recent fecal contamination in temperate regions (e.g. Servais et al., 2007; Ouattarra et al., 2013). In tropical ecosystems they have also been used to monitor contamination levels despite reports that free-living coliforms may be indigenous to some tropical waters and can’t be distinguished from those from a fecal source (Carillo et al., 1985; Jiminez et al., 1989). Indeed, Rochelle-Newall et al (2015) noted that our ability to culture FIB (eg, E.coli and faecal coliforms) and the ability of these FIB to become naturalized in the environment are two of the most important factors for deciding whether or not we can estimate correctly FIB and the pathogens for which they are indicators. Ideally, methods that monitor faecal contamination without having to rely on culturing techniques are required. The use of specific biomarkers for fecal contamination such as stannols is one such option (Solecki et al., 2011; Jeanneau et al., 2012). However, while these methods have the advantage that they are culture-independent and species specific (chicken, pig or human); they have the disadvantage that they require considerable analytical technologies that are often lacking in developing countries (Rochelle-Newall et al., 2015).
Today, the most commonly measured bacterial indicators are Total coliforms, Faecal Coliforms, and Escherichia coli. Total coliforms are a group of bacteria that are widespread in nature, which are found in the soil, in many environments water, in human feces or animal manure, submerged wood and in other places outside the human body. Thus, the usefulness of total coliforms as an indicator of fecal contamination depends on the extent to which the bacteria species found (Willden, 2006). Fecal Coliforms are a form of of total coliform bacteria, and as its name implies, it originates from fecal matter. E. coli is a species of fecal coliform bacteria that is specific to fecal material from humans and other warm-blooded animals. Leclerc et al. (2001) proposed that the use of E. coli is the best indicator of the presence of pathogenic bacteria and fecal contamination. In environmental waters, several studies have reported significant correlations between indicators of fecal pollution. For example, Donze (2004) reported that there was a significant positive relationship between total coliforms and E. coli (r = 0.59, N = 30, p < 0.001). Byamukama et al (2000), in a study from the Nakivubo channel, Uganda, that all microbiological parameters (total, fecal coliforms and E. coli) were significantly correlated. Wilkes et al (2009) also found, in a comparative study on the presence and concentration of several pathogenic and indicator bacteria in the surface water of a Canadian river, that significant correlations were found total coliforms and E. coli. It therefore seems that although it is preferable to used E.coli as an indicator of recent fecal contamination, given the correlations between the coliforms and E.coli, that in the absence of E.coli numbers, faecal and total coliform numbers can be used to indicator the presence of possible faecal contamination.

Primary sources of FIB

The microbiological quality of rivers is primarily controlled by human and animal activities in the watershed. Humans, livestock and wild animals are all primary sources of faecal contamination (Fig. 3.1) although human faecal waste has the highest risk of waterborne disease, since the probability of human pathogens being present is highest. In urban areas, faecal microorganisms are mainly brought to aquatic environments through the discharge of treated and untreated domestic and industrial wastewaters (Servais et al., 2007b). Point sources (outfall of wastewater treatment or industrial plants and open sewer outlets) are often a major source of pollution in urbanized and industrialized catchments. Servais et al. (2007b) showed that in a large urbanized watershed (Seine, France), the input of fecal microorganisms from non-point sources is much lower than the inputs from point sources. These authors also examined the links between land use and FIB concentrations. They looked at surface runoff and leaching under three types of land use: forest areas, cultivated areas and grassland areas and found that small streams draining pastures were significantly more contaminated (around 1000 FC 100ml-1) than those draining forests or cultivated areas (around 100 FC 100ml-1).
In temperate regions with industrial scale agriculture, the microbial loading potential from point sources, such as storage facilities and feedlots, and from non-point sources, such as grazed pastures and rangelands, can be substantial (Table 3.1). Muirhead et al. (2005) in an experimental study of surface runoff from cowpats found E. coli concentrations of 1 x 106 MPN 100ml-1 and other workers have reported concentrations of up to an order more. High numbers of E. coli from animals and wildlife can reach surface waters in agricultural watersheds where direct excretion and runoff of fecal material from manure can enter waterways (Crowther et al., 2002; Kloot, 2007; Vidon et al., 2008a).
In developing countries and particularly in rural areas, agriculture is less intensive, wastewater treatment is often absent and non-point sources tend to predominate and the primary source of FIB is faecal matter generated by domestic and wild animals. For example, Ribolzi et al. (2011) and Causse et al. (2015), working in rural Laos, found that E. coli concentrations were below 1 MPN 100ml-1 in the upper areas of the watershed indicating a very low background level of contamination that was probably caused by wildlife. However, as the density of poultry and humans settlements increased in the downstream areas, values of up 230 MPN 100ml-1 were found. Other non-agricultural sources of microbial pollution in rural watersheds include failing septic systems and latrine overflows during periods of heavy rain, all of which can create health problems in the downstream human populations. However, as a consequence of their dispersion, these non-point sources of microbial pollution are inherently more difficult to identify andcharacterize than point sources.
FIB and the water borne pathogens for which they are an indicator are particularly susceptible to shifts in hydrology and water quality (Vidon et al., 2008b; Cho et al., 2010; Chu et al., 2011). Stormwater discharges are a major cause of rapid deterioration in surface water quality. Storm events increase turbidity, suspended solids, organic matter and faecal contamination in rivers and streams, although the microbiological quality of stormwater varies widely and reflects human activities in the watershed (Ribolzi et al., 2011; Causse et al., 2015; 52 Ekklesia et al., 2015). Geldreich (1991) reported that stormwater in combined sewers can have more than 10-fold higher thermotolerant coliform levels than in separate stormwater sewers.
In rural areas and in urban areas without adequate wastewater treatment or stormflow management, one of the major pathways via which faecal contaminants enter waterways is via overland flow. Overland flow occurs when rainfall is unable to infiltrate the soil surface and runs over the ground, normally in rivulets. Overland flow is also the predominant means by which soil particles and faecal contamination in soils are transported from land to surface waters. The concentrations of FIB in overland flow are controlled by many factors such as rainfall duration and intensity, manure application, faecal deposit age and type, adsorption to soil particles, etc. (Blaustein et al., 2015; Rochelle-Newall et al., 2015).
Many authors have highlighted the low contribution of groundwater to FIB concentrations (Jamieson et al., 2004). These low values are probably as a result of efficient soil filtering of microorganisms in infiltrating water (Matthess et al., 1988), in contrast to overland flow characterized by high FIB concentrations.The values of only 4 E.coli 100 ml-1 found in groundwater of a village in Laosis far lower than the reported values of 230 000 E.coli 100 ml-1 in overland flow during a storm downstream of a small stream (Ribolzi et al., 2011).
In stream sediments have also been identified as a reservoir for E. coli. Many studies indicate that sediments harbor much higher populations of both Faecal coliforms (FC) and E. coli than the overlying water (e.g. Rehmann and Soupir, 2009; Chu et al., 2011; Pachepsky and Shelton, 2011). Mechanical disturbance of bottom sediments, as occurs during flood events can cause increased E. coli concentrations in the overlying waters as a result of their resuspension (Cho et al., 2010). Muirhead et al. (2004), during an artificial flood experiment, observed that E. coli concentrations peaked ahead of the flow peak, consistent with the entrainment of FC into the water column from underlying contaminated sediments by accelerating currents on the rising 53 limb of the hydrograph. A two order of magnitude increase was observed during the event. E.coli concentrations were correlated with turbidity over the flood event, however, when turbidity returned to base levels between each flood, E. coli concentrations remained elevated. A similar dynamic was observed by Ribolzi et al. (2016a),who conducted a detailed examination of E.coli dynamics during a flood in an upland stream. By separating the groundwater and overland flow components of the flood they were able to identify the contribution of sediments to the total E.coli numbers in the stream. They showed that up to 75% of the E.coli in the stream were from the sediments and not from soil runoff from the sloping lands above the stream.

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Table of contents :

1 General Introduction
1.1. Human activities, microbial pathogens and organic carbon
1.1.1 Aims and scientific questions of the thesis
1.1.2 Structure of the thesis
2 Study site and Methods
2.1 Study site
2.1.1 Water resources in Viet Nam
2.1.2 Red River Basin
2.2 Methods
2.2.1 Sampling strategy and laboratory analysis
2.2.2 Seneque/Riverstrahler model
2.2.3 Principles of the Riverstrahler model
3 Faecal indicator bacteria
3.1 Faecal indicator bacteria
3.1.1 Introduction and definition
3.1.2 Primary sources of FIB
3.1.3 Secondary sources of FIB
3.1.4 Fate in the aquatic continuum
3.2 Seasonal variability of faecal indicator bacteria numbers and die-off rates in the Red River basin, North Viet Nam (Article 1)
3.2.1 Abstract
3.2.2 Introduction
3.2.3 Materials and methods
3.2.4 Results
3.2.5 Discussion
3.2.6 Conclusions
3.3 Modeling of Faecal Indicator Bacteria (FIB) in the Red River basin, North Viet Nam (Article 2):
3.3.1 Abstract
3.3.2 Introduction
3.3.3 Material and methods
3.3.4 Results and discussion
3.3.5 Conclusions
4 Organic carbon
4.1 Organic carbon in aquatic systems
4.1.1 Introduction and definition
4.1.2 Sources
4.1.3 Role of climate
4.1.4 Biodegradability of DOC
4.2 Organic carbon transfers in the subtropical Red River system (Viet Nam). Insights on CO2 sources and sinks (Article 3).
4.2.1 Abstract
4.2.2 Introduction
4.2.3 Material and methods
4.2.4 Results
4.2.5 Discussion
4.2.6 Conclusion
5 General conclusions and perspectives
5.1 General conclusions
5.2 Directions for future research
6 References
7 Appendices
7.1 Appendix I: List of publications in international journals of Rank A
7.2 Appendix II: List of oral and poster presentations at conferences and seminars
7.3 Appendix III: List of conference proceedings

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