Village Settlements in Mountainous Tropical Areas, Hotspots of Fecal Contamination as Evidenced by Escherichia coli and Stanol Concentrations in Stormwater Pulses.

Fecal bacteria in surface water may indicate threats to human health. Our hypothesis is that village settlements in tropical rural areas are major hotspots of fecal contamination because of the number of domestic animals usually roaming in the alleys and the lack of fecal matter treatment before entering the river network. By jointly monitoring the dynamics of Escherichia coli and of seven stanol compounds during four flood events (July-August 2016) at the outlet of a ditch draining sewage and surface runoff out of a village of Northern Lao PDR, our objectives were (1) to assess the range of E. coli concentration in the surface runoff washing off from a village settlement and (2) to identify the major contributory sources of fecal contamination using stanol compounds during flood events. E. coli pulses ranged from 4.7 × 104 to 3.2 × 106 most probable number (MPN) 100 mL-1, with particle-attached E. coli ranging from 83 to 100%. Major contributory feces sources were chickens and humans (about 66 and 29%, respectively), with the highest percentage switching from the human pole to the chicken pole during flood events. Concentrations indicate a severe fecal contamination of surface water during flood events and suggest that villages may be considered as major hotspots of fecal contamination pulses into the river network and thus as point sources in hydrological models.

The Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys.

Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns.

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Modelling of faecal indicator bacteria (FIB) in the Red River basin (Vietnam).

Many studies have been published on the use of models to assess water quality through faecal contamination levels. However, the vast majority of this work has been conducted in developed countries and similar studies from developing countries in tropical regions are lacking. Here, we used the Seneque/Riverstrahler model to investigate the dynamics and seasonal distribution of total coliforms (TC), an indicator of faecal contamination, in the Red River (Northern Vietnam) and its upstream tributaries. The results of the model showed that, in general, the overall correlations between the simulated and observed values of TC follow a 1:1 relationship at all examined stations. They also showed that TC numbers were affected by both land use in terms of human and livestock populations and by hydrology (river discharge). We also developed a possible scenario based on the predicted changes in future demographics and land use in the Red River system for the 2050 horizon. Interestingly, the results showed only a limited increase of TC numbers compared with the present situation at all stations, especially in the upstream Vu Quang station and in the urban Ha Noi station. This is probably due to the dominance of diffuse sources of contamination relative to point sources. The model is to our knowledge one of the first mechanistic models able to simulate spatial and seasonal variations of microbial contamination (TC numbers) in the whole drainage network of a large regional river basin covering both urban and rural areas of a developing country.

Nutrient ratios and the complex structure of phytoplankton communities in a highly turbid estuary of Southeast Asia.

Phytoplankton diversity and abundance in estuarine systems are controlled by many factors. Salinity, turbidity, and inorganic nutrient concentrations and their respective ratios have all been proposed as principal factors that structure phytoplankton diversity and influence the emergence of potentially toxic species. Although much work has been conducted on temperate estuaries, less is known about how phytoplankton diversity is controlled in tropical, monsoonal systems that are subject to large, seasonal shifts in hydrology and to rapidly changing land use. Here, we present the results of an investigation into the factors controlling phytoplankton species composition and distribution in a tropical, monsoonal estuary (Bach Dang estuary, North Vietnam). A total of 245 taxa, 89 genera from six algal divisions were observed. Bacillariophyceae were the most diverse group contributing to 51.4 % of the microalgal assemblage, followed by Dinophyceae (29.8 %), Chlorophyceae (10.2 %), Cyanophyceae (3.7 %), Euglenophyceae (3.7 %) and Dictyochophyceae (1.2 %). The phytoplankton community was structured by inorganic nutrient ratios (DSi:DIP and DIN:DIP) as well as by salinity and turbidity. Evidence of a decrease in phytoplankton diversity concomitant with an increase in abundance and dominance of certain species (e.g., Skeletonema costatum) and the appearance of some potentially toxic species over the last two decades was also found. These changes in phytoplankton diversity are probably due to a combination of land use change resulting in changes in nutrient ratios and concentrations and global change as both rainfall and temperature have increased over the last two decades. It is therefore probable in the future that phytoplankton diversity will continue to change, potentially favoring the emergence of toxic species in this system.

Metal contamination, their ecological risk, and relationship with other variables in surface sediments of urban rivers in a big city in Asia: case study of Hanoi, Vietnam.

Urban rivers are significantly impacted by anthropogenic pressure. This study presents the updated assessment of the concentrations of 11 metals and other variables (pH, total organic carbon (TOC) and nutrients (total nitrogen, total phosphorus, and total silica)) in the sediments of four urban rivers in inner Hanoi city, Vietnam, during the period 2020-2022. The mean concentrations of Fe, Zn, As, and Cr were higher than the permissible values of the Vietnam National technical regulation on the surface sediment quality. Moreover, Zn and Cr were at the severe effect level of the US EPA guidelines for sediment quality. The calculation of pollution indices (Igeo and EF) demonstrated that Mn, Ni, and Fe were from natural sources whereas other metals were from both anthropogenic and natural sources. The ecological risk index revealed that metals in Hanoi riverine sediments were classified at considerable ecological risk. High values of metals, TOC, and nutrients in the sediments of these urban rivers mostly originate from the accumulation of untreated urban wastewater that is enhanced by low river discharge. Our results may provide scientific base for better management decisions to ensure environmental protection and sustainable development of Hanoi city.

Microbial contamination in the coastal aquaculture zone of the Ba Lat river mouth, Vietnam.

Contamination of aquaculture products by pathogenic organisms is a major concern in areas where this activity is of high economic importance. The abundances of total coliforms (TC), Escherichia coli (EC) and faecal streptococci (FS) (in CFU.100 mL-1) in seawater in the Red River coastal aquaculture zone were determined. The results showed TC numbers (200 to 9100; average 1822), EC (<100 to 3400; average 469) and FS (<100 to 2100; average 384), of which TC exceeded the allowable threshold of the Vietnam regulation for coastal aquaculture water. TC and EC numbers in 4 wastewater types (domestic, livestock farming sewage, agricultural runoff, and mixed sewage canals) were investigated and revealed the importance of point sources of faecal contamination in seawater. These results underline the need to reduce the release of untreated wastewater and to put into place seawater microbial quality monitoring in areas where the development of sustainable aquaculture is an objective.

Distribution of Burkholderia pseudomallei within a 300-cm deep soil profile: implications for environmental sampling.

The environmental distribution of Burkholderia pseudomallei, the causative agent of melioidosis, remains poorly understood. B. pseudomallei is known to have the ability to occupy a variety of environmental niches, particularly in soil. This paper provides novel information about a putative association of soil biogeochemical heterogeneity and the vertical distribution of B. pseudomallei. We investigated (1) the distribution of B. pseudomallei along a 300-cm deep soil profile together with the variation of a range of soil physico-chemical properties; (2) whether correlations between the distribution of B. pseudomallei and soil physico-chemical properties exist and (3) when they exist, what such correlations indicate with regards to the environmental conditions conducive to the occurrence of B. pseudomallei in soils. Unexpectedly, the highest concentrations of B. pseudomallei were observed between 100 and 200 cm below the soil surface. Our results indicate that unravelling the environmental conditions favorable to B. pseudomallei entails considering many aspects of the actual complexity of soil. Important recommendations regarding environmental sampling for B. pseudomallei can be drawn from this work, in particular that collecting samples down to the water table is of foremost importance, as groundwater persistence appears to be a controlling factor of the occurrence of B. pseudomallei in soil.

Evaluation of heavy metal contamination in the coastal aquaculture zone of the Red River Delta (Vietnam).

Coastal aquaculture contributes significantly to the local economy of many countries however water quality issues in the coastal regions are threatening the sustainability of this economic activity. This paper presents the analysis of seven heavy metals (HM) in surface seawater and wastewater from the Red River coastal aquaculture zone during 2019-2020. HM concentrations (µg.L-1) from 72 seawater samples were: Zn: 60.76 (0.5-188.0); Cu: 26.91 (0.10-96.0); Pb: 7.27 (0.8-31.2); Cr: 6.71 (0.6-28.4); As: 1.38 (0.15-5.78); Cd: 0.44 (0.04-2.41); and Hg: 0.34 (0.02-1.39). All mean values of HM in seawater were lower than the Vietnam regulatory limits for aquaculture seawater although high individual HM concentrations were found in some isolated seawater samples. Concerning wastewater quality, only mean As concentration was higher than the Vietnam regulatory limit for surface water quality, despite the fact that high concentrations of other individual HM were observed. The PCA analysis on the entire dataset of seawater and wastewater samples revealed that HM concentrations in seawater originate from various sources including human activities and natural conditions. The total potential ecological risk index (averaging 18.6; from 7.48 to 39.05) for the Red River coastal zone is in the low range. These results provide a scientific basis for better management of the coastal environment which is important for the sustainable development of the aquaculture industry in this area.

Viral distribution and life strategies in the Bach Dang Estuary, Vietnam.

Although the structure and dynamics of planktonic viruses in freshwater and seawater environments are relatively well documented, little is known about the occurrence and activity of these viruses in estuaries, especially in the tropics. Viral abundance, life strategies, and morphotype distribution were examined in the Bach Dang Estuary (Vietnam) during the dry season in 2009. The abundance of both viruses and their prokaryotic hosts decreased significantly from upstream to downstream, probably as the result of nutrient dilution and osmotic stress faced by the freshwater communities. The antibiotic mitomycin-C revealed that the fraction of lysogenic cells was substantially higher in the lower seawater part of the estuary (max 27.1%) than in the upper freshwater area where no inducible lysogens were observed. The question of whether there is a massive, continuous induction of marine lysogens caused by the mixing with freshwater is considered. Conversely, the production of lytic viruses declined as salinity increased, indicating a spatial succession of viral life strategies in this tropical estuary. Icosahedral tailless viruses with capsids smaller than 60 nm dominated the viral assemblage throughout the estuary (63.0% to 72.1% of the total viral counts), and their distribution was positively correlated with that of viral lytic production. Interestingly, the gamma-proteobacteria explained a significant portion of the variance in the <60 nm and 60 to 90 nm tailless viruses (92% and 80%, respectively), and in the Myoviridae (73%). Also, 60% of the variance of the tailless larger viruses (>90 nm) was explained by the beta-proteobacteria. Overall, these results support the view that the environment, through selection mechanisms, probably shapes the structure of the prokaryotic community. This might be in turn a source of selection for the virioplankton community via specific affiliation favoring particular morphotypes and life strategies.

Environmental determinants of E. coli, link with the diarrheal diseases, and indication of vulnerability criteria in tropical West Africa (Kapore, Burkina Faso).

In 2017, diarrheal diseases were responsible for 606 024 deaths in Sub-Saharan Africa. This situation is due to domestic and recreational use of polluted surface waters, deficits in hygiene, access to healthcare and drinking water, and to weak environmental and health monitoring infrastructures. Escherichia coli (E. coli) is an indicator for the enteric pathogens that cause many diarrheal diseases. The links between E. coli, diarrheal diseases and environmental parameters have not received much attention in West Africa, and few studies have assessed health risks by taking into account hazards and socio-health vulnerabilities. This case study, carried out in Burkina Faso (Bagre Reservoir), aims at filling this knowledge gap by analyzing the environmental variables that play a role in the dynamics of E. coli, cases of diarrhea, and by identifying initial vulnerability criteria. A particular focus is given to satellite-derived parameters to assess whether remote sensing can provide a useful tool to assess the health hazard. Samples of surface water were routinely collected to measure E. coli, enterococci and suspended particulate matter (SPM) at a monitoring point (Kapore) during one year. In addition, satellite data were used to estimate precipitation, water level, Normalized Difference Vegetation Index (NDVI) and SPM. Monthly epidemiological data for cases of diarrhea from three health centers were also collected and compared with microbiological and environmental data. Finally, semi-structured interviews were carried out to document the use of water resources, contact with elements of the hydrographic network, health behavior and condition, and water and health policy and prevention, in order to identify the initial vulnerability criteria. A positive correlation between E. coli and enterococci in surface waters was found indicating that E. coli is an acceptable indicator of fecal contamination in this region. E. coli and diarrheal diseases were strongly correlated with monsoonal precipitation, in situ SPM, and Near Infra-Red (NIR) band between March and November. Partial least squares regression showed that E. coli concentration was strongly associated with precipitation, Sentinel-2 reflectance in the NIR and SPM, and that the cases of diarrhea were strongly associated with precipitation, NIR, E. coli, SPM, and to a lesser extent with NDVI. Moreover, E. coli dynamics were reproduced using satellite data alone, particularly from February to mid-December (R2 = 0.60) as were cases of diarrhea throughout the year (R2 = 0.76). This implies that satellite data could provide an important contribution to water quality monitoring. Finally, the vulnerability of the population was found to increase during the rainy season due to reduced accessibility to healthcare and drinking water sources and increased use of water of poor quality. During this period, surface water is used because it is close to habitations, easy to use and free from monetary or political constraints. This vulnerability is aggravated by marginality and particularly affects the Fulani, whose concessions are often close to surface water (river, lake) and far from health centers.

Experimental and modelling evidence of splash effects on manure borne Escherichia coli washoff.

In tropical montane South-East Asia, recent changes in land use have induced increased runoff, soil erosion and in-stream suspended sediment loads. Land use change is also contributing to increased microbial pathogen dissemination and contamination of stream waters. Escherichia coli (E. coli) is frequently used as an indicator of faecal contamination. Field rain simulations were conducted to examine how E. coli is exported from the surface of upland, agricultural soils during runoff events. The objectives were to characterize the loss dynamics of this indicator from agricultural soils contaminated with livestock waste, and to identify the effect of splash on washoff. Experiments were performed on nine 1 m2 plots, amended or not with pig or poultry manure. Each plot was divided into two 0.5 m2 sub-plots. One of the two sub-plots was protected with a mosquito net for limiting the raindrop impact effects. Runoff, soil detachment by raindrop impact and its entrainment by runoff, and E. coli loads and discharge were measured for each sub-plot. The results show that raindrop impact strongly enhances runoff generation, soil detachment and entrainment and E. coli export. When the impact of raindrops was reduced with a mosquito net, total runoff was reduced by more than 50%, soil erosion was on average reduced by 90% and E. coli export from the amended soil surface was on average 3 to 8 times lower. A coupled physics-based approach was performed using the Cast3M platform for modelling the time evolutions of runoff, solid particles detachment and transfer and bacteria transport that were measured for one of the nine plots. After estimation of the saturated hydraulic conductivity, soil erodibility and attachment rate of bacteria, model outputs were consistent with measured runoff coefficients, suspended sediment and E. coli loads. This work therefore underlines the need to maintain adequate vegetation at the soil surface to avoid the erosion and export of soil borne potential pathogens towards downstream aquatic systems.

Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR.

In the basin of Mekong, over 70 million people rely on unimproved surface water for their domestic requirements. Surface water is often contaminated with fecal matter and yet little information exists on the underlying mechanisms of fecal contamination in tropical conditions at large watershed scales. Our objectives were to (1) investigate the seasonality of fecal contamination using Escherichia coli as fecal indicator bacteria (FIB), and (2) establish links between the fecal contamination in stream water and its controlling factors (hydrology and land use). We present the results of (1) a sampling campaign at the outlet of 19 catchments across Lao PDR, in both the dry and the rainy seasons of 2016, and (2) a 10-day interval monitoring conducted in 2017 and 2018 at three point locations of three rivers (Nam Ou, Nam Suang, and Mekong) in northern Lao PDR. Our results show the presence of fecal contamination at most of the sampled sites, with a seasonality characterized by higher and extreme E. coli concentrations occurring during the rainy season. The highest E. coli concentrations, strongly correlated with total suspended sediment concentrations, were measured in catchments dominated by unstocked forest areas, especially in mountainous northern Lao PDR and in Vientiane province.

Antibiotics in surface water of East and Southeast Asian countries: A focused review on contamination status, pollution sources, potential risks, and future perspectives.

This review provides focused insights into the contamination status, sources, and ecological risks associated with multiple classes of antibiotics in surface water from the East and Southeast Asia based on publications over the period 2007 to 2020. Antibiotics are ubiquitous in surface water of these countries with concentrations ranging from <1 ng/L to hundreds µg/L and median values from 10 to 100 ng/L. Wider ranges and higher maximum concentrations of certain antibiotics were found in surface water of the East Asian countries like China and South Korea than in the Southeast Asian nations. Environmental behavior and fate of antibiotics in surface water is discussed. The reviewed occurrence of antibiotics in their sources suggests that effluent from wastewater treatment plants, wastewater from aquaculture and livestock production activities, and untreated urban sewage are principal sources of antibiotics in surface water. Ecological risks associated with antibiotic residues were estimated for aquatic organisms and the prevalence of antibiotic resistance genes and antibiotic-resistant bacteria were reviewed. Such findings underline the need for synergistic efforts from scientists, engineers, policy makers, government managers, entrepreneurs, and communities to manage and reduce the burden of antibiotics and antibiotic resistance in water bodies of East and Southeast Asian countries.

Polysaccharide aggregation as a potential sink of marine dissolved organic carbon.

The formation and sinking of biogenic particles mediate vertical mass fluxes and drive elemental cycling in the ocean. Whereas marine sciences have focused primarily on particle production by phytoplankton growth, particle formation by the assembly of organic macromolecules has almost been neglected. Here we show, by means of a combined experimental and modelling study, that the formation of polysaccharide particles is an important pathway to convert dissolved into particulate organic carbon during phytoplankton blooms, and can be described in terms of aggregation kinetics. Our findings suggest that aggregation processes in the ocean cascade from the molecular scale up to the size of fast-settling particles, and give new insights into the cycling and export of biogeochemical key elements such as carbon, iron and thorium.

Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.

To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3-V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.

Urban ecology, stakeholders and the future of ecology.

The world human population is more and more urban and cities have a strong impact on the biosphere. This explains the development of urban ecology. In this context, the goal of our work is fourfold: to describe the diversity of scientific questions in urban ecology, show how these questions are organized, to assess how these questions can be built in close interactions with stakeholders, to better understand the role urban ecology can play within ecological sciences. A workshop with scientists from all relevant fields (from ecology to sociology) and stakeholders was organized by the Foundation for Research on Biodiversity (FRB). Three types of scientific issues were outlined about (1) the biodiversity of organisms living in urban areas, (2) the functioning of urban organisms and ecosystems, (3) interactions between human societies and urban ecological systems. For all types of issues we outlined it was possible to distinguish both fundamental and applied scientific questions. This allowed building a unique research agenda encompassing all possible types of scientific issues in urban ecology. As all types of ecological and evolutionary questions can be asked in urban areas, urban ecology will likely be more and more influential in the development of ecology. Taken together, the future of towns, their biodiversity and the life of city dwellers is at stake. Increasing the space for ecosystems and biodiversity within towns is more and more viewed as crucial for the well-being of town dwellers. Depending on research and the way its results are taken into account, very different towns could emerge. Urban areas can be viewed as a test and a laboratory for the future of the interactions between human and ecological systems.

Vicinal land use change strongly drives stream bacterial community in a tropical montane catchment.

Impact of land use (LU) change on stream environmental conditions and the inhabiting bacterial community remains rarely investigated, especially in tropical montane catchments. We examined the effects of LU change and its legacy along a tropical stream by comparing seasonal patterns of dissolved organic carbon (DOC) / colored dissolved organic matter (CDOM) in relation to variations in structure, diversity and metabolic capacities of particle-attached (PA) and free-living (FL) bacterial communities. We hypothesized that despite seasonal differences, hydrological flows that accumulate allochthonous carbon along the catchment are a major controlling factor of the bacterial community. Surprisingly, local environmental conditions that were largely related to nearby LU and the legacy of LU change were more important for stream bacterial diversity than hydrological connectivity. DOC was strongly correlated with PA richness and diversity. The legacy of LU change between teak plantation and annual crops induced high DOC and high diversity and richness of PA in the adjacent waters, while banana plantations were associated with high diversity of FL. The community structures of both PA and FL differed significantly between seasons. Our results highlight the importance of vicinal LU change and its legacy on aquatic bacterial communities in mixed used tropical watersheds.

Hydrological modeling of Fecal Indicator Bacteria in a tropical mountain catchment.

The occurrence of pathogen bacteria in surface waters is a threat to public health worldwide. In particular, inadequate sanitation resulting in high contamination of surface water with pathogens of fecal origin is a serious issue in developing countries such as Lao P.D.R. Despite the health implications of the consumption of contaminated surface water, the environmental fate and transport of pathogens of fecal origin and their indicators (Fecal Indicator Bacteria or FIB) are still poorly known in tropical areas. In this study, we used measurements of flow rates, suspended sediments and of the FIB Escherichia coli (E. coli) in a 60-ha catchment in Northern Laos to explore the ability of the Soil and Water Assessment Tool (SWAT) to simulate watershed-scale FIB fate and transport. We assessed the influences of 3 in-stream processes, namely bacteria deposition and resuspension, bacterial regrowth, and hyporheic exchange (i.e. transient storage) on predicted FIB numbers. We showed that the SWAT model in its original version does not correctly simulate small E. coli numbers during the dry season. We showed that model's performance could be improved when considering the release of E. coli together with sediment resuspension. We demonstrated that the hyporheic exchange of bacteria across the Sediment-Water Interface (SWI) should be considered when simulating FIB concentration not only during wet weather, but also during the dry season, or baseflow period. In contrast, the implementation of the regrowth process did not improve the model during the dry season without inducing an overestimation during the wet season. This work thus underlines the importance of taking into account in-stream processes, such as deposition and resuspension, regrowth and hyporheic exchange, when using SWAT to simulate FIB dynamics in surface waters.

Use of fallout radionuclides ((7)Be, (210)Pb) to estimate resuspension of Escherichia coli from streambed sediments during floods in a tropical montane catchment.

Consumption of water polluted by faecal contaminants is responsible for 2 million deaths annually, most of which occur in developing countries without adequate sanitation. In tropical aquatic systems, streambeds can be reservoirs of persistent pathogenic bacteria and high rainfall can lead to contaminated soils entering streams and to the resuspension of sediment-bound microbes in the streambed. Here, we present a novel method using fallout radionuclides ((7)Be and (210)Pbxs) to estimate the proportions of Escherichia coli, an indicator of faecal contamination, associated with recently eroded soil particles and with the resuspension of streambed sediments. We show that using these radionuclides and hydrograph separations we are able to characterize the proportion of particles originating from highly contaminated soils and that from the resuspension of particle-attached bacteria within the streambed. We also found that although overland flow represented just over one tenth of the total flood volume, it was responsible for more than two thirds of the downstream transfer of E. coli. We propose that data obtained using this method can be used to understand the dynamics of faecal indicator bacteria (FIB) in streams thereby providing information for adapted management plans that reduce the health risks to local populations. Graphical Abstract Graphical abstract showing (1) the main water flow processes (i.e. overland flow, groundwater return flow, blue arrows) and sediment flow components (i.e. resuspension and soil erosion, black arrows) during floods in the Houay Pano catchment; (2) the general principle of the method using fallout radionuclide markers (i.e. (7)Be and (210)Pbxs) to estimate E. coli load from the two main sources (i.e. streambed resuspension vs soil surface washoff); and 3) the main results obtained during the 15 May 2012 storm event (i.e. relative percentage contribution of each process to the total streamflow, values in parentheses).