Effect of streambed bacteria release on E. coli concentrations: Monitoring and modeling with the modified SWAT

Multiscale spatiotemporal variability of fecal indicator bacteria and associated particle size distributions in the sandy bottom sediments of a Pennsylvania creek

Concentrations of the fecal indicator bacteria (FIB) Escherichia coli and enterococci are used to assess microbial impairment in irrigation and recreation water sources. Although the FIB concentrations' variability at large temporal scales, such as seasons, and large spatial scales encompassing different land use has been studied, the knowledge about smaller scale variability remains sparse. This work aimed to research the small-scale variability of E. coli and enterococci in a montane creek with sandy bottom sediments. Sediment samples were collected weekly for a year in triplicate at sampling sites in a forested headwater, an agricultural area, and a mixed urban-agricultural area. The average weekly change in concentrations was from two times at the forested site to five times at the urban-agricultural site. Mean relative deviations from averages across sampling locations increased from -25% at the forested site to 45% at the urban-agricultural site. This trend was also observed separately over the cold and warm seasons. Over a week without precipitation, E. coli concentrations decreased on average by 20% in warm period and by 45% in cold period; the enterococci concentration declined by 12% in both cold and warm periods. The sediment particle size distributions were significantly different among the three sites and between the cold and warm seasons. Rankings of sediment fine mass fractions and FIB concentrations were positively correlated at two of three sampling sites in more than 70% of observation dates. The results of this work indicate the need to evaluate the uncertainty of sediment FIB concentrations before designing sediment FIB monitoring quality.

Cultivating Food Safety Together: Insights About the Future of Produce Safety in the U.S. Controlled Environment Agriculture Sector

Controlled environment agriculture (CEA) is a rapidly growing sector that presents unique challenges and opportunities in ensuring food safety. This manuscript highlights critical gaps and needs to promote food safety in CEA systems as identified by stakeholders (n=47) at the Strategizing to Advance Future Extension andResearch (S.A.F.E.R.) CEA conference held in April 2023 at The Ohio State University's Ohio CEA Research Center. Feedback collected at the conference was analyzed using an emergent thematic analysis approach to determine key areas of focus. Research-based guidance is specific to the type of commodity, production system type, and size. Themes include the need for improved supply chain control, cleaning, and sanitization practices, pathogen preventive controls and mitigation methods and training and education. Discussions surrounding supply chain control underscored the significance of the need for approaches to mitigate foodborne pathogen contamination. Effective cleaning and sanitization practices are vital to maintaining a safe production environment, with considerations such as establishing standard operating procedures, accounting for hygienic equipment design, and managing the microbial communities within the system. Data analysis further highlights the need for risk assessments, validated pathogen detection methods, and evidence-based guidance in microbial reduction. In addition, training and education were identified as crucial in promoting a culture of food safety within CEA. The development of partnerships between industry, regulatory, and research institutions are needed to advance data-driven guidance and practices across the diverse range of CEA operations and deemed essential for addressing challenges and advancing food safety practices in CEA. Considering these factors, the CEA industry can enhance food safety practices, foster consumer trust, and support its long-term sustainability.

(Antibiotic-Resistant) E. coli in the Dutch-German Vecht Catchment─Monitoring and Modeling

Fecally contaminated waters can be a source for human infections. We investigated the occurrence of fecal indicator bacteria (E. coli) and antibiotic-resistant E. coli, namely, extended spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-EC) and carbapenemase-producing E. coli (CP-EC) in the Dutch-German transboundary catchment of the Vecht River. Over the course of one year, bacterial concentrations were monitored in wastewater treatment plant (WWTP) influents and effluents and in surface waters with and without WWTP influence. Subsequently, the GREAT-ER model was adopted for the prediction of (antibiotic-resistant) E. coli concentrations. The model was parametrized and evaluated for two distinct scenarios (average flow scenario, dry summer scenario). Statistical analysis of WWTP monitoring data revealed a significantly higher (factor 2) proportion of ESBL-EC among E. coli in German compared to Dutch WWTPs. CP-EC were present in 43% of influent samples. The modeling approach yielded spatially accurate descriptions of microbial concentrations for the average flow scenario. Predicted E. coli concentrations exceed the threshold value of the Bathing Water Directive for a good bathing water quality at less than 10% of potential swimming sites in both scenarios. During a single swimming event up to 61 CFU of ESBL-EC and less than 1 CFU of CP-EC could be taken up by ingestion.

Quantifying the effects of land use change and aggregate stormwater management practices on fecal coliform dynamics in a temperate catchment

Changes in land use and land cover (LULC) due to land development can lead to an increase in diffuse microbial pollutions and, consequently, degradation of the receiving aquatic ecosystem. However, the mechanisms underlying these phenomena are rarely considered in hydrological models. Therefore, in this study, fecal indicator bacteria (FIB) and total suspended solids (TSS) in a temperate catchment were simulated using a well-established water quality model (Personal Computer Storm Water Management Model) to systematically quantify the factors influencing their dynamics and the effects of stormwater management. Additionally, high-resolution data (e.g., water quality variables and LULC changes) were used to calibrate the model, which accurately reproduced the physical and biological features of the catchment. The results showed that increases in bare land areas and impervious cover in the catchment exceeded the Korean (as well as the USEPA-based) standard recreational water quality criteria for fecal contamination and TSS. Dissolved organic compounds (only during storm events), TSS, and total nitrogen (except during the pre-development phase) were the strongest predictors in shaping FIB dynamics. The multiple control of stormwater management reduced the FIB and TSS concentrations by approximately 65% in the catchment. The results of this study not only provide conclusions on the drivers of FIB and TSS dynamics and their quantitative contribution but also help in designing a methodology for empirical and ecological predictions of diffuse microbial and TSS pollution in a catchment with ongoing land development.

Quantitative microbial human exposure model for faecal indicator bacteria and risk assessment of pathogenic Escherichia coli in surface runoff following application of dairy cattle slurry and co-digestate to grassland

Animal waste contains high numbers of microorganisms and therefore can present a potential biological threat to human health. During episodic rainfall events resulting in runoff, microorganisms in the waste and soil may migrate into surface runoff, contaminating surface water resources. A probabilistic human exposure (HE) model was created to determine exposure to faecal indicator bacteria (FIB): total coliforms (TC), E. coli and enterococci following application of bio-based fertiliser (dairy cattle slurry, digestate) to grassland; using a combination of experimental field results and literature-based data. This step was followed by a quantitative microbial risk assessment (QMRA) model for pathogenic E. coli based on a literature-based dose-response model. The results showed that the maximum daily HE (HE_daily) is associated with E. coli for unprocessed slurry (treatment T1) on day 1, the worst-case scenario where the simulated mean HE_daily was calculated as 2.84 CFU day ^-1. The results indicate that the overall annual probability of risk (P_annual) of illness from E. coli is very low or low based on the WHO safe-limit of P_annual as 10 ^-6. In the worst-case scenario, a moderate risk was estimated with simulated mean P_annual as 1.0 × 10 ^-5. Unpasteurised digestate application showed low risk on day 1 and 2 (1.651 × 10 ^-6, 1.167 × 10 ^-6, respectively). Pasteurised digestate showed very low risk in all scenarios. These results support the restriction imposed on applying bio-based fertiliser if there is any rain forecast within 48 h from the application time. This study proposes a future extension of the probabilistic model to include time, intensity, discharge, and distance-dependant dilution factor. The information generated from this model can help policymakers ensure the safety of surface water sources through the quality monitoring of FIB levels in bio-based fertiliser.

Verifying the applicability of SWAT to simulate fecal contamination for watershed management of Selangor River, Malaysia

The Soil and Water Assessment Tool (SWAT) ecohydrological model was utilized to simulate fecal contamination in the 1937 km² Selangor River Watershed in Malaysia. The watershed conditions posed considerable challenges owing to data scarcity and tropical climate conditions, which are very different from the original conditions that SWAT was developed and tested for. Insufficient data were compensated by publicly available data (e.g., land cover, soil, and weather) to run SWAT. In addition, field monitoring and interviews clarified representative situations of pollution sources and loads, which were used as input for the model. Model parameters determined by empirical analyses in the USA (e.g., surface runoff, evapotranspiration, and temperature adjustment for bacteria die-off) are thoroughly discussed. In particular, due consideration was given to tropical climate characteristics such as intense rainfall, high potential evapotranspiration, and high temperatures throughout the year. As a result, the developed SWAT successfully simulated fecal contamination ranging several orders of magnitude along with its spatial distribution (i.e., Nash-Sutcliffe Efficiency (NSE) = 0.64, Root Mean Square Error-Observations Standard Deviation Ratio (RSR) = 0.64 at six mainstem sites, and NSE = 0.67 and RSR = 0.57 at 12 major tributaries). Moreover, mitigation countermeasures for future worsening of fecal contamination (i.e., E.coli concentration > 20,000 CFU/100 mL for 690 days during nine years at a raw water intake point for Kuala Lumpur [KL] residents) were analyzed through scenario simulations, thereby contributing to discussing effective watershed management. The results propose improving decentralized sewage treatment systems and treating chicken manure with effective microorganisms in order to guarantee water safety for KL residents (i.e., E.coli concentrations <20,000 CFU/100 mL throughout the period, considering Malaysian standards). Accordingly, this study verified the applicability of SWAT to simulate fecal contamination in areas that are difficult to model and suggests solutions for watershed management based on quantitative evidence.

Impacts of rapid urbanization on characteristics, sources and variation of fecal coliform at watershed scale

Microbial pollution is an environmental problem of growing concern for threatening human health. However, the impacts of rapid urbanization on characteristics, sources and variation of fecal coliform (FC) at watershed scale have not been fully explored. In this study, FC characteristics were monitored monthly for 2 years at 21 river sections in an urbanizing watershed, while the sources and continuously annual variation were quantified by integrating two commonly-used models. The results showed that FC varied from 10³ to 10⁶ MPN/L, indicating a great spatiotemporal variation at watershed scale. Peak FC occurred in summer and autumn among upstream and downstream areas, respectively. Besides, 65% impermeable surface was identified as the threshold of urban level, beyond which the key FC source would shift from agriculture to urban. It was also found that the changes of urban landscape patterns had poor correlation with annual variation of FC. In comparison, urbanization speed was identified as the major driver with the threshold of 30% for deteriorating FC pollution. The Low Impact Development could result in a 5.13%-97.59% reduction of FC at watershed scale.

Sediment and fecal indicator bacteria loading in a mixed land use watershed: Contributions from suspended sediment and bedload transport

Overland transport of fecal bacteria in water and their resuspension from bed sediments are important transport mechanisms that help explain the transport of enteric pathogens in watersheds. In this study, multiyear monitoring along with regression relationships between sediment and fecal indicator bacteria (FIB) were used to investigate annual loading in the South Fork Broad River watershed, located in northeastern Georgia, USA. Suspended transport was the dominant transport mechanism contributing to in-stream total annual loads for sediment (81.4-98.1%) and FIB (>98%). Annual bedload transport of FIB was small and Escherichia coli (up to 1.8%) contributed more to annual bedload FIB than enterococci (≤0.03%). Bedload contributions of FIB increased with the duration of critical discharge exceedance, indicating a prolonged risk of exposure to enteric pathogens during extended periods of high flows, which is important during major storm events. The risk of exposure to enteric pathogens through pathways such as recreational use and drinking water treatment could be much greater because fecal bacteria are released from sediment during higher flows and dominantly transported in suspension when bedload are not actively moving. Therefore, the combined contribution of fecal bacteria from overland and bedload-associated transport should be considered in risk assessments. Discharge, bedload, and FIB data collected over 2 yr in this study can supplement future hydrologic modeling and microbial risk assessment modeling efforts.

Reliability theory for microbial water quality and sustainability assessment

Microbial surface water contamination can disrupt critical ecosystem services such as recreation and drinking water supply. Prediction of water contamination and assessment of sustainability of water resources in the context of water quality are needed but are difficult to achieve - with challenges arising from the complexity of environmental systems, and stochastic variability of processes that drive contaminant fate and transport. In this paper we use reliability theory as a framework to address these issues. We define failure as exceedance of regulatory water contamination limits, and system components as reaches in the surface water network. We then methodically study the reliability of each component in the context of water quality, as well as the impact of individual components on overall water quality and sustainability. We obtain spatially distributed probability- and physics-based sustainability measures of reliability, vulnerability, resilience and the sustainability index. Finally, we use GIS as a platform to present these measures as geospatial products in an effort to foster public acceptance of probability-based methods in contaminant hydrology.

Evaluation of the soil and water assessment tool (SWAT) for simulating E. coli concentrations at the watershed-scale

Water quality management at the watershed level requires a framework to identify sources, apportion water quality risks and develop mitigation strategies to reduce health risks. Watershed-scale models have been used as a support tool to understand the sources, fate and transport of fecal bacteria and pathogens in the environment. The Soil and Water Assessment Tool (SWAT) model was applied in this study to understand the sources and drivers of microbial water quality in the Clouds Creek watershed in Georgia, USA. A criterion to evaluate the performance of the SWAT bacterial model was also developed in this study using the Nash-Sutcliffe Efficiency (NSE) performance measure. The SWAT model was successfully calibrated and validated for flow with Nash-Sutcliffe Efficiency (NSE) of 0.81 and 0.55, respectively. Escherichia coli (E. coli) predictions were good with NSE of 0.32 and 0.34 for the calibration and validation timeframes, respectively. Based on the criteria developed in this study, SWAT bacterial model for E. coli and fecal coliform can be judged as "satisfactory" when NSE > 0.20. The contribution of sources followed this order: in-stream cattle manure deposition > cattle manure application > poultry manure application > septic systems > wildlife manure, suggesting that a reduction in livestock access to streams would be the most effective approach to reduce fecal bacterial loads in this watershed and others impacted by fecal contamination. Finally, our results suggest that the SWAT model is capable of simulating E. coli dynamics in the Clouds Creek watershed and can provide insights into source impacts for risk management.

Chronic urban hotspots and agricultural drainage drive microbial pollution of karst water resources in rural developing regions

Contamination of surface and groundwater systems with human and animal faecal matter leads to exposure of reliant populations to disease causing micro-organisms. This exposure route remains a major cause of infection and mortality in developing countries, particularly rural regions. To meet the UN's sustainable development goal 6: Ensure availability and sustainable management of water and sanitation for all, we need to identify the key controls on faecal contamination across relevant settings. We conducted a high-resolution spatial study of E. coli concentration in catchment drainage waters over 6 months in a mixed land-use catchment in the extensive karst region extending across impoverished southwest China. Using a mixed effects modelling framework, we tested how land-use, karst hydrology, antecedent meteorological conditions, agricultural cycles, hydrochemistry, and position in the catchment system affected E. coli concentrations. Land-use was the best predictor of faecal contamination levels. Sites in urban areas were chronically highly contaminated, but water draining from agricultural land was also consistently contaminated and there was a catchment wide pulse of higher E. coli concentrations, turbidity, and discharge during paddy field drainage. E. coli concentration increased with increasing antecedent rainfall across all land-use types and compartments of the karst hydrological system (underground and surface waters), but decreased with increasing pH. This is interpreted to be a result of processes affecting pH, such as water residence time, rather than the direct effect of pH on E. coli survival. Improved containment and treatment of human waste in areas of higher population density would likely reduce contamination hotspots, and further research is needed to identify the nature and distribution of sources in agricultural land.

Particle association of Enterococcus sp. increases growth rates and simulated persistence in water columns of varying light attenuation and turbulent diffusivity

Predicting water quality and the human health risks associated with sewage-derived microbes requires understanding the fate and transport of these contaminants. Sewage-derived pathogen risks are typically assessed and monitored by measuring concentrations of fecal indicating bacteria (FIB), like Enterococcus sp. Previous research demonstrated that a high fraction of FIB is particle-associated, which can alter FIB dynamics within secondary water bodies. In this study, we experimentally quantified the effect of particle association on dark, temperature- and light-dependent growth and sinking rates of enterococci. Particle association significantly increased dark growth rates, light-dependent growth rates (i.e. decreased mortality), and sinking rates, relative to free-living enterococci. Simulations using a novel, 1-dimensional model parameterized by these rates indicate greater persistence (T₉₀) for particle-associated enterococci in water bodies across a wide range of diffuse attenuation coefficients of light (K_d) and turbulent diffusivity (D) values. In addition, persistence of both fractions increased in simulated turbid and turbulent waters, compared to clear and/or quiescent conditions. Simulated persistence of both fractions also increased when enterococci discharges occurred later in a diel cycle (towards sunset, as opposed to sunrise), especially for the free-living population, because later discharges under our model conditions allowed both fractions to mix deeper before inactivation via sunlight. Model sensitivity testing revealed that T₉₀ variability was greatest when dark growth rates were altered, suggesting that future empirical studies should focus on quantifying these rates for free-living and particle-associated sewage-derived microbes. Despite greater sensitivity of T₉₀ to variability in dark growth rates, omitting light-dependent growth rates from simulations dramatically influenced T₉₀ values. Our results demonstrate that particle association can increase enterococci persistence in receiving waters and highlight the importance of incorporating particle association in future water quality models.

An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 1: Background and model description

A new Model for the Agent-based simulation of Faecal Indicator Organisms (MAFIO) is developed that attempts to overcome limitations in existing faecal indicator organism (FIO) models arising from coarse spatial discretisations and poorly-constrained hydrological processes. MAFIO is a spatially-distributed, process-based model presently designed to simulate the fate and transport of agents representing FIOs shed by livestock at the sub-field scale in small (<10 km²) agricultural catchments. Specifically, FIO loading, die-off, detachment, surface routing, seepage and channel routing are modelled on a regular spatial grid. Central to MAFIO is that hydrological transfer mechanisms are simulated based on a hydrological environment generated by an external model for which it is possible to robustly determine the accuracy of simulated catchment hydrological functioning. The spatially-distributed, tracer-aided ecohydrological model EcH₂O-iso is highlighted as a possible hydrological environment generator. The present paper provides a rationale for and description of MAFIO, whilst a companion paper applies the model in a small agricultural catchment in Scotland to provide a proof-of-concept.

Spatiotemporal variability and key influencing factors of river fecal coliform within a typical complex watershed

Fecal coliform bacteria are a key indicator of human health risks; however, the spatiotemporal variability and key influencing factors of river fecal coliform have yet to be explored in a rural-suburban-urban watershed with multiple land uses. In this study, the fecal coliform concentrations in 21 river sections were monitored for 20 months, and 441 samples were analyzed. Multivariable regressions were used to evaluate the spatiotemporal dynamics of fecal coliform. The results showed that spatial differences were mainly dominated by urbanization level, and environmental factors could explain the temporal dynamics of fecal coliform in different urban patterns except in areas with high urbanization levels. Reducing suspended solids is a direct way to manage fecal coliform in the Beiyun River when the natural factors are difficulty to change, such as temperature and solar radiation. The export of fecal coliform from urban areas showed a quick and sensitive response to rainfall events and increased dozens of times in the short term. Landscape patterns, such as the fragmentation of impervious surfaces and the overall landscape, were identified as key factors influencing urban non-point source bacteria. The results obtained from this study will provide insight into the management of river fecal pollution.

Prediction of recreational water safety using Escherichia coli as an indicator: case study of the Passaic and Pompton rivers, New Jersey

As contact with high concentrations of pathogens in a waterbody can cause waterborne diseases, Escherichia coli is commonly used as an indicator of water quality in routine public health monitoring of recreational freshwater ecosystems. However, traditional processes of detection and enumeration of pathogen indicators can be costly and are not time-sensitive enough to alarm recreational users. The predictive models developed to produce real-time predictions also have various methodological challenges, including arbitrary selection of explanatory variables, deterministic statistical approach, and heavy reliance on correlation instead of the more rigorous multivariate regression analyses, among others. The objective of this study is to address these challenges and develop a cost-effective and timely alternative for estimating pathogen indicators using real-time water quality and quantity data. As a case study we use New Jersey, where pathogens represent the most common cause of impairment for water quality, and Passaic and Pompton rivers, which are among the largest in the state and the country. We used Membrane Filtration Method and mColiblue24 media to enumerate Escherichia coli in a total of 69 water samples collected from April to November 2016 from the two rivers. We also collected data on environmental variables concurrently and performed stepwise and logistic regression analyses to address the said methodological challenges and determine the variables significantly predicting whether or not the Escherichia coli count was above prescribed levels for recreation activities. The results show that source water, higher specific conductance, lower pH, and cumulative rainfall for the 72 h antecedent the sampling significantly impacted the density of Escherichia coli. In addition to using the Bagging technique to validate the results, we also assessed Whole Model Tests, R², Entropy R², and Misclassification Rates. This approach improves the prediction of bacteria counts and their use in informing the potential safety/hazard of that waterbody for recreational activities.

Temporal stability of E. coli and Enterococci concentrations in a Pennsylvania creek

Microbial quality of irrigation waters is a substantial food safety factor. Escherichia coli (E. coli) and Enterococci are used as the fecal indicator bacteria (FIB) to assess microbial water quality. Analysis of temporally stable patterns of FIB can facilitate effective monitoring of microbial water quality. The objectives of this study were (1) to investigate the spatiotemporal variation of E. coli and Enterococci concentrations in a large creek traversing diverse land use areas and (2) to explore the presence of temporally stable FIB concentration patterns along the creek. Concentrations of both FIB were measured weekly at five water monitoring locations along the 20-km long creek reach in Pennsylvania at baseflow for three years. The temporal stability was assessed using mean relative deviations of logarithms of FIB concentration from the average across the reach measured at the same time. The Spearman rank correlation coefficients between logarithms of FIB concentrations on consecutive sampling times was another metric used to assess the temporal stability of FIB concentration patterns. Logarithms of FIB concentrations had sinusoidal dependence on time and significantly correlated with temperature at all locations Both FIB exhibited temporal stability of concentrations. The two most downstream locations in urbanized areas tended to have logarithms of concentrations higher than the average along the observation reach. The location in the upstream forested area had mostly lower concentrations (log E. coli 1.59, log Enterococci 1.69) than average (log E. coli 2.07, log Enterococci 2.20). concentrations in colony-forming units (CFU) (100 mL)^-1. Two locations in the agricultural and sparsely urbanized area had these logarithm values close to the average. The temporal stability was more pronounced in cold seasons than in warm seasons. No significant difference was found between pattern determined for each of three observation years and for the entire three-year observation period. The Spearman rank correlations between observations on consecutive dates showed moderate to very strong relationships in most cases. Existence of the temporal stability of FIB concentrations in the creek indicates locations that inform about the average logarithm of concentrations or the geometric mean concentrations along the entire observation reach.

Modeling the Effects of Future Hydroclimatic Conditions on Microbial Water Quality and Management Practices in Two Agricultural Watersheds

Anticipated future hydroclimatic changes are expected to alter the transport and survival of fecally-sourced waterborne pathogens, presenting an increased risk of recreational water quality impairments. Managing future risk requires an understanding of interactions between fecal sources, hydroclimatic conditions and best management practices (BMPs) at spatial scales relevant to decision makers. In this study we used the Hydrologic Simulation Program FORTRAN to quantify potential fecal coliform (FC - an indicator of the potential presence of pathogens) responses to a range of mid-century climate scenarios and assess different BMP scenarios (based on reduction factors) for reducing the risk of water quality impairment in two, small agricultural watersheds - the Chippewa watershed in Minnesota, and the Tye watershed in Virginia. In each watershed, simulations show a wide range of FC responses, driven largely by variability in projected future precipitation. Wetter future conditions, which drive more transport from non-point sources (e.g. manure application, livestock grazing), show increases in FC loads. Loads typically decrease under drier futures; however, higher mean FC concentrations and more recreational water quality criteria exceedances occur, likely caused by reduced flow during low-flow periods. Median changes across the ensemble generally show increases in FC load. BMPs that focus on key fecal sources (e.g., runoff from pasture, livestock defecation in streams) within a watershed can mitigate the effects of hydroclimatic change on FC loads. However, more extensive BMP implementation or improved BMP efficiency (i.e., higher FC reductions) may be needed to fully offset increases in FC load and meet water quality goals, such as total maximum daily loads and recreational water quality standards. Strategies for managing climate risk should be flexible and to the extent possible include resilient BMPs that function as designed under a range of future conditions.

A REVIEW OF WATER QUALITY RESPONSES TO AIR TEMPERATURE AND PRECIPITATION CHANGES 1: FLOW, WATER TEMPERATURE, SALTWATER INTRUSION

Anticipated future increases in air temperature and regionally variable changes in precipitation will have direct and cascading effects on U.S. water quality. In this paper, and a companion paper by Coffey et al. (2019), we review technical literature addressing the responses of different water quality attributes to historical and potential future changes in air temperature and precipitation. The goal is to document how different attributes of water quality are sensitive to these drivers, to characterize future risk to inform management responses and to identify research needs to fill gaps in our understanding. Here we focus on potential changes in streamflow, water temperature, and salt water intrusion (SWI). Projected changes in the volume and timing of streamflow vary regionally, with general increases in northern and eastern regions of the U.S., and decreases in the southern Plains, interior Southwest and parts of the Southeast. Water temperatures have increased throughout the U.S. and are expected to continue to increase in the future, with the greatest changes in locations where high summer air temperatures occur together with low streamflow volumes. In coastal areas, especially the mid-Atlantic and Gulf coasts, SWI to rivers and aquifers could be exacerbated by sea level rise, storm surges, and altered freshwater runoff. Management responses for reducing risks to water quality should consider strategies and practices robust to a range of potential future conditions.

Depth-Dependent Response of Fecal Indicator Bacteria in Sediments to Changes in Water Column Nutrient Levels

Concentrations of in bottom sediments can influence the assessment of microbial stream water quality. Runoff events bring nutrients to streams that can support the growth of in sediments. The objective of this work was to evaluate depth-dependent changes in populations after nutrients are introduced to the water column. Bovine feces were collected fresh and mixed into sediment. Studies were performed in a microcosm system with continuous flow of synthetic stream water over inoculated sediment. Dilutions of autoclaved bovine manure were added to water on Day 16 at two concentrations, and KBr tracer was introduced into the water column to evaluate ion diffusion. Concentrations of , total coliforms, and total aerobic heterotrophic bacteria, along with orthophosphate-P and ammonium N, were monitored in water and sediment for 32 d. Sediment samples were analyzed in 0- to 1-cm and 1- to 3-cm sectioned depths. Concentrations of and total coliforms in top sediments were approximately one order of magnitude greater than in bottom sediments throughout the experiment. Introduction of nutrients to the water column triggered an increase of nutrient levels in both top and bottom sediments and increased concentrations of bacteria in the water. However, the added nutrients had a limited effect on in sediment where bacterial inactivation continued. Vertical gradients of concentrations in sediments persisted during the inactivation periods both before and after nutrient addition to the water column.

Event-transport of beta-d-glucuronidase in an agricultural headwater stream: Assessment of seasonal patterns by on-line enzymatic activity measurements and environmental isotopes

Understanding the fate of fecal pollution in the landscape is required for microbial risk analysis. The aim of this study was to assess the patterns and dynamics of beta-d-glucuronidase (GLUC), which has been suggested as a surrogate for fecal pollution monitoring, in a stream draining an agricultural headwater catchment. Automated enzymatic on-site measurements of stream water and sediments were made over two years (2014-2016) to quantify the sources and pathways of GLUC in a stream. The event water fraction of streamflow was estimated by stable isotopes. Samples from field sediments on a hillslope, streambed sediment and stream water were analyzed for GLUC and with a standard E. coli assay. The results showed ten times higher GLUC and E. coli concentrations during the summer than during the winter for all compartments (field and streambed sediments and stream water). The E. coli concentrations in the streambed sediment were approximately 100 times those of the field sediments. Of the total GLUC load in the study period, 39% were transported during hydrological events (increased streamflow due to rainfall or snowmelt); of these, 44% were transported when the stream contained no recent rainwater. The results suggested that a large proportion of the GLUC and E. coli in the stream water stemmed from resuspended streambed sediments. Moreover, the results strongly indicated the existence of remnant populations of GLUC-active organisms in the catchment.

Factors affecting the spatial and temporal distribution of E. coli in intertidal estuarine sediments

Microbiological water quality monitoring of bathing waters does not account for faecal indicator organisms in sediments. Intertidal deposits are a significant reservoir of FIOs and this indicates there is a substantial risk to bathers through direct contact with the sediment, or through the resuspension of bacteria to the water column. Recent modelling efforts include sediment as a secondary source of contamination, however, little is known about the driving factors behind spatial and temporal variation in FIO abundance. E. coli abundance, in conjunction with a wide range of measured variables, was used to construct models to explain E. coli abundance in intertidal sediments in two Scottish estuaries. E. coli concentrations up to 6 log₁₀ CFU 100 g dry wt^-1 were observed, with optimal models accounting for E. coli variation up to an adjusted R² of 0.66. Introducing more complex models resulted in overfitting of models, detrimentally affected the transferability of models between datasets. Salinity was the most important single variable, with season, pH, colloidal carbohydrates, organic content, bulk density and maximum air temperature also featuring in optimal models. Transfer of models, using only lower cost variables, between systems explained an average deviance of 42%. This study demonstrates the potential for cost-effective sediment characteristic monitoring to contribute to FIO fate and transport modelling and consequently the risk assessment of bathing water safety.

Patterns of sediment-associated fecal indicator bacteria in an urban estuary: Benthic-pelagic coupling and implications for shoreline water quality

Estuarine and coastal waterways are commonly monitored for fecal and sewage contamination to protect recreator health and ecosystem functions. Such monitoring programs commonly rely on cultivation-based counts of fecal indicator bacteria (FIB) in water column samples. Recent studies demonstrate that sediments and beach sands can be heavily colonized by FIB, and that settling and resuspension of colonized particles may significantly influence the distribution of FIB in the water column. However, measurements of sediment FIB are rarely incorporated into monitoring programs, and geographic surveys of sediment FIB are uncommon. In this study, the distribution of FIB and the extent of benthic-pelagic FIB coupling were examined in the urbanized, lower Hudson River Estuary. Using cultivation-based enumeration, two commonly-measured FIB, enterococci and Escherichia coli, were widely distributed in both sediment and water, and were positively correlated with each other. The taxonomic identity of FIB isolates from water and sediment was confirmed by DNA sequencing. The geometric mean of FIB concentration in sediment was correlated with both the geometric mean of FIB in water samples from the same locations and with sediment organic carbon. These two positive associations likely reflect water as the FIB source for underlying sediments, and longer FIB persistence in the sediments compared to the water, respectively. The relative representation of other fecal associated bacterial genera in sediment, determined by 16S rRNA gene sequencing, increased with the sequence representation of the two FIB, supporting the value of these FIB for assessing sediment contamination. Experimental resuspension of sediment increased shoreline water column FIB concentrations, which may explain why shoreline water samples had higher average FIB concentrations than samples collected nearby but further from shore. In combination, these results demonstrate extensive benthic-pelagic coupling of FIB in an urbanized estuary and highlight the importance of sediment FIB distribution and ecology when interpreting water quality monitoring data.

The Environmental Impact of Cattle Access to Watercourses: A Review

The degradation of freshwater resources and loss of freshwater biodiversity by anthropogenic activities, including agriculture, are of major global concern. Together with diffuse pollutants, point sources, such as where cattle have direct access to riparian margins and watercourses, can potentially present significant environmental challenges. These can include impacts on stream morphology, increased sedimentation, nutrient additions, microbial contamination, and impacts on aquatic biota. Mitigation measures aimed at reducing these frequently include reducing the amount of time cattle spend in riparian margins and watercourses. This is often accomplished through the provision of an alternative water supply and grazing management, or even cattle exclusion measures. Although a number of studies refer to potential negative impacts, there has been little attempt to review previous research on this topic. The key aim of this paper is to collate and review these disparate studies, as well as those relating to the effectiveness of mitigation measures. Although it is difficult to draw generalizations from studies due to the inherent variability between and within catchments, evidence pertaining to impacts in relation to sedimentation, pathogens, and riparian margin vegetation were strong. Conclusions in relation to impacts on stream morphology and nutrient parameters were less clear, whereas studies on responses of macroinvertebrate communities were particularly variable, with differences due to cattle access difficult to separate from catchment scale effects. A greater understanding of the impact of cattle access on watercourses under varying conditions will help inform policymakers on the cost effectiveness of existing management criteria and will help in revising existing measures.

How can we improve understanding of faecal indicator dynamics in karst systems under changing climatic, population, and land use stressors? - Research opportunities in SW China

Human exposure to water contaminated with faeces is a leading cause of worldwide ill-health. Contaminated water can be transmitted rapidly in karst terrain as a result of the connectivity of surface and groundwater systems, high transmissivity of aquifers over large areas, and well-developed underground conduit systems. Faecal indicator organisms (FIOs) are the most widely-used indicator of faecal contamination and microbial water quality; however, the conceptualisation of FIO risk and associated sources, pathways, and survival dynamics of FIOs in karst landscapes requires a degree of modification from traditional conceptual models of FIO fate and transfer in non-karst systems. While a number of reviews have provided detailed accounts of the state-of-the-science concerning FIO dynamics in catchments, specific reference to the uniqueness of karst and its influence on FIO fate and transfer is a common omission. In response, we use a mixed methods approach of critical review combined with a quantitative survey of 372 residents of a typical karst catchment in the southwest China karst region (SWCKR) to identify emerging research needs in an area where much of the population lives in poverty and is groundwater dependent. We found that the key research needs are to understand: 1) overland and subsurface FIO export pathways in karst hydrology under varying flow conditions; 2) urban and agricultural sources and loading in mixed land-use paddy farming catchments; 3) FIO survival in paddy farming systems and environmental matrices in karst terrain; 4) sediment-FIO interactions and legacy risk in karst terrain; and 5) key needs for improved hydrological modelling and risk assessment in karst landscapes. Improved knowledge of these research themes will enable the development of evidence-based faecal contamination mitigation strategies for managing land and water resources in the SWCKR, which is highly vulnerable to climate change impacts on water supply and quality of water resources.

A REVIEW OF WATER QUALITY RESPONSES TO AIR TEMPERATURE AND PRECIPITATION CHANGES 2: NUTRIENTS, ALGAL BLOOMS, SEDIMENT, PATHOGENS

In this paper we review the published, scientific literature addressing the response of nutrients, sediment, pathogens and cyanobacterial blooms to historical and potential future changes in air temperature and precipitation. The goal is to document how different attributes of water quality are sensitive to these drivers, to characterize future risk, to inform management responses and to identify research needs to fill gaps in our understanding. Results suggest that anticipated future changes present a risk of water quality and ecosystem degradation in many U.S. locations. Understanding responses is, however, complicated by inherent high spatial and temporal variability, interactions with land use and water management, and dependence on uncertain changes in hydrology in response to future climate. Effects on pollutant loading in different watershed settings generally correlate with projected changes in precipitation and runoff. In all regions, increased heavy precipitation events are likely to drive more episodic pollutant loading to water bodies. The risk of algal blooms could increase due to an expanded seasonal window of warm water temperatures and the potential for episodic increases in nutrient loading. Increased air and water temperatures are also likely to affect the survival of waterborne pathogens. Responding to these challenges requires understanding of vulnerabilities, and management strategies to reduce risk.

Spatially explicit pollutant load-integrated in-stream E. coli concentration modeling in a mixed land-use catchment

Pathogen contamination is a major cause of surface water impairment in the United States, and fecal bacteria levels are typically used to evaluate microbial loading in bodies of water. Environmental models are considered a useful tool for evaluating watershed management practices. In this study, we assessed E. coli contamination of the Upper Stroubles Creek, Virginia, USA using the Soil and Water Assessment Tool (SWAT) model. The study area has been declared an impaired body of water due to recent bacterial contamination. Bacterial source characterizations play a critical role in such modeling exercises and especially in the case of non-point sources. As the SWAT model involves bacteria load estimation at a Hydrological Response Unit (HRU) level, we use the Spatially Explicit Load Enrichment Calculation Tool (SELECT) for our E. coli load estimations. We also evaluate current approaches to the measurement of bacterial interactions of the sediment-water interface using SWAT and the frequent measurements of streambed E. coli concentrations. For the simulation of in-stream E. coli concentrations using estimates drawn from SELECT without (with) sediment bacteria resuspension-deposition, Nash-Sutcliffe Efficiency (NSE) values of -0.41 to 0.34 (-0.19 to 0.36) are found. Moreover, in-stream E. coli concentrations measured at flow duration intervals show that the model frequently overestimates mid-range flows while underestimating low-range flows even with model improvements. The use of high-resolution E. coli loads and the consideration of sediment bacteria resuspension-deposition processes, generated higher E. coli concentrations for forested areas compared to those of urban and pasture lands, suggesting the importance of using detailed bacteria load estimations and land use information when assessing E. coli distribution in the environment.

Modeling the Impact of Land Use Change on Basin-scale Transfer of Fecal Indicator Bacteria: SWAT Model Performance

Land use change from annual crops to commercial tree plantations can modify flow and transport processes at the watershed scale, including the fate and transport of fecal indicator bacteria (FIB), such as . The Soil and Water Assessment Tool (SWAT) is a useful means for integrating watershed characteristics and simulating water and contaminants. The objective of this study was to provide a comprehensive assessment of the impact of land use change on microbial transfer from soils to streams using the SWAT model. This study was conducted for the Houay Pano watershed located in northern Lao People's Democratic Republic. Under the observed weather conditions, the SWAT model predicted a decrease from 2011 to 2012 and an increase from 2012 to 2013 in surface runoff, suspended solids, and transferred from the soil surface to streams. The amount of precipitation was important in simulating surface runoff, and it subsequently affected the fate and transport of suspended solids and bacteria. In simulations of identical weather conditions and different land uses, fate and transport was more sensitive to the initial number of than to its drivers (i.e., surface runoff and suspended solids), and leaf area index was a significant factor influencing the determination of the initial number of on the soil surface. On the basis of these findings, this study identifies several limitations of the SWAT fertilizer and bacteria modules and suggests measures to improve our understanding of the impacts of land use change on FIB in tropical watersheds.

Particle attached and free floating pathogens survival kinetics under typical stream and thermal spring temperature conditions

Improved understanding of pathogen survival in the stream environment is needed to enhance existing predictive models of stream pathogen populations. Further, the increasing use of thermal springs for bathing necessitates additional studies focused on not only typical streams but also thermal spring conditions, where water temperature is relatively higher than typical streams. This study was conducted to assess the survival of E. coli O157:H7 and Salmonella Typhimurium in stream water under free floating and particle-attached conditions at a range of temperature. A series of microcosm studies were conducted to determine pathogen decay rates. In bench-scale experiments, water circulation and sediment resuspension mimicked natural stream and thermal spring conditions, with continuous air flow providing aeration, constant mixing and turbulent conditions, and improved water circulation. Data on E. coli O157:H7 and Salmonella survival were subsequently used to determine first-order decay equations for calculating the rate constant and decimal reduction time for the modeled experimental conditions. Results showed that at 40 °C, the survival of particle attached E. coli O157:H7 was longer than that of particle attached Salmonella. Under free floating condition, Salmonella survived longer than E. coli O157:H7. At 50 °C, survival of particle attached E. coli O157:H7 and Salmonella was longer than that of free floating E. coli and Salmonella. At 60 °C, survival of particle attached Salmonella was longer than that of free floating Salmonella. Similarly at 60 °C, the survival of E. coli O157:H7  under particle attached condition was longer than that of the free floating condition. The findings of this study suggest that the survival of E. coli O157:H7 differs than the survival of Salmonella in stream water and thermal spring conditions, and the assumption used in previous studies to estimate survival of bacteria in stream environment could result in over/underestimation if the impact of particle attachment on pathogen survival is not accounted for.

Development and evaluation of the bacterial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

The Agricultural Policy/Environmental eXtender (APEX) is a watershed-scale water quality model that includes detailed representation of agricultural management. The objective of this work was to develop a process-based model for simulating the fate and transport of manure-borne bacteria on land and in streams with the APEX model. The bacteria model utilizes manure erosion rates to estimate the amount of edge-of-field bacteria export. Bacteria survival in manure is simulated as a two-stage process separately for each manure application event. In-stream microbial fate and transport processes include bacteria release from streambeds due to sediment resuspension during high flow events, active release from the streambed sediment during low flow periods, bacteria settling with sediment, and survival. Default parameter values were selected from published databases and evaluated based on field observations. The APEX model with the newly developed microbial fate and transport module was applied to simulate fate and transport of the fecal indicator bacterium Escherichia coli in the Toenepi watershed, New Zealand that was monitored for seven years. The stream network of the watershed ran through grazing lands with daily bovine waste deposition. Results show that the APEX with the bacteria module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water as affected by various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations.

Remote collection of microorganisms at two depths in a freshwater lake using an unmanned surface vehicle (USV)

Microorganisms are ubiquitous in freshwater aquatic environments, but little is known about their abundance, diversity, and transport. We designed and deployed a remote-operated water-sampling system onboard an unmanned surface vehicle (USV, a remote-controlled boat) to collect and characterize microbes in a freshwater lake in Virginia, USA. The USV collected water samples simultaneously at 5 and 50 cm below the surface of the water at three separate locations over three days in October, 2016. These samples were plated on a non-selective medium (TSA) and on a medium selective for the genus Pseudomonas (KBC) to estimate concentrations of culturable bacteria in the lake. Mean concentrations ranged from 134 to 407 CFU/mL for microbes cultured on TSA, and from 2 to 8 CFU/mL for microbes cultured on KBC. There was a significant difference in the concentration of microbes cultured on KBC across three sampling locations in the lake (P = 0.027), suggesting an uneven distribution of Pseudomonas across the locations sampled. There was also a significant difference in concentrations of microbes cultured on TSA across the three sampling days (P = 0.038), demonstrating daily fluctuations in concentrations of culturable bacteria. There was no significant difference in concentrations of microbes cultured on TSA (P = 0.707) and KBC (P = 0.641) across the two depths sampled, suggesting microorganisms were well-mixed between 5 and 50 cm below the surface of the water. About 1 percent (7/720) of the colonies recovered across all four sampling missions were ice nucleation active (ice+) at temperatures warmer than −10 °C. Our work extends traditional manned observations of aquatic environments to unmanned systems, and highlights the potential for USVs to understand the distribution and diversity of microbes within and above freshwater aquatic environments.

Microcosms for evaluating microbial indicator persistence and mobilization in fluvial sediments during rainfall events

Mediterranean rivers, which are subject to long, dry periods and heavy rainfall events, could be particularly useful for understanding future climate scenarios. This study generated microcosms that mimicked riverbank sediment resuspension into the water of a typical Mediterranean river as a consequence of heavy rainfall. The mobilization and inactivation of six fecal pollution indicators and microbial source tracking markers were evaluated. The T₉₀ values in the sediments were: 4 days for sorbitol-fermenting Bifidobacterium, 11 days for culturable E. coli, 36 days for bacteriophages infecting Bacteroides thetaiotaomicron strain GA17 and more than 42 days for qPCR-detected E. coli, somatic coliphages and sulfite-reducing clostridia spores. Bacteriophages and bacteria showed different resuspension and sedimentation patterns. The data obtained could be used in predictive models to assess the effects of climate change on surface water quality. Pathogen mobilization into the water column poses a risk for humans, animals and the natural environment, and breaches the One Health approach.

Escherichia coli attachment to model particulates: The effects of bacterial cell characteristics and particulate properties

E. coli bacteria move in streams freely in a planktonic state or attached to suspended particulates. Attachment is a dynamic process, and the fraction of attached microorganisms is thought to be affected by both bacterial characteristics and particulate properties. In this study, we investigated how the properties of cell surfaces and stream particulates influence attachment. Attachment assays were conducted for 77 E. coli strains and three model particulates (ferrihydrite, Ca-montmorillonite, or corn stover) under environmentally relevant conditions. Surface area, particle size distribution, and total carbon content were determined for each type of particulate. Among the three particulates, attachment fractions to corn stover were significantly larger than the attachments to 2-line ferrihydrite (p-value = 0.0036) and Ca-montmorillonite (p-value = 0.022). Furthermore, attachment to Ca-montmorillonite and corn stover was successfully modeled by a Generalized Additive Model (GAM) using cell characteristics as predictor variables. The natural logarithm of the net charge on the bacterial surface had a significant, positive, and linear impact on the attachment of E. coli bacteria to Ca-montmorillonite (p-value = 0.013), but it did not significantly impact the attachment to corn stover (p-value = 0.36). The large diversities in cell characteristics among 77 E. coli strains, particulate properties, and attachment fractions clearly demonstrated the inadequacy of using a static parameter or linear coefficient to predict the attachment behavior of E. coli in stream water quality models.

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.

Predicting fecal coliform using the interval-to-interval approach and SWAT in the Miyun watershed, China

Pathogens in manure can cause waterborne-disease outbreaks, serious illness, and even death in humans. Therefore, information about the transformation and transport of bacteria is crucial for determining their source. In this study, the Soil and Water Assessment Tool (SWAT) was applied to simulate fecal coliform bacteria load in the Miyun Reservoir watershed, China. The data for the fecal coliform were obtained at three sampling sites, Chenying (CY), Gubeikou (GBK), and Xiahui (XH). The calibration processes of the fecal coliform were conducted using the CY and GBK sites, and validation was conducted at the XH site. An interval-to-interval approach was designed and incorporated into the processes of fecal coliform calibration and validation. The 95% confidence interval of the predicted values and the 95% confidence interval of measured values were considered during calibration and validation in the interval-to-interval approach. Compared with the traditional point-to-point comparison, this method can improve simulation accuracy. The results indicated that the simulation of fecal coliform using the interval-to-interval approach was reasonable for the watershed. This method could provide a new research direction for future model calibration and validation studies.

Riverbed Sediments as Reservoirs of Multiple Vibrio cholerae Virulence-Associated Genes: A Potential Trigger for Cholera Outbreaks in Developing Countries

Africa remains the most cholera stricken continent in the world as many people lacking access to safe drinking water rely mostly on polluted rivers as their main water sources. However, studies in these countries investigating the presence of Vibrio cholerae in aquatic environments have paid little attention to bed sediments. Also, information on the presence of virulence-associated genes (VAGs) in environmental ctx-negative V. cholerae strains in this region is lacking. Thus, we investigated the presence of V. cholerae VAGs in water and riverbed sediment of the Apies River, South Africa. Altogether, 120 samples (60 water and 60 sediment samples) collected from ten sites on the river (January and February 2014) were analysed using PCR. Of the 120 samples, 37 sediment and 31 water samples were positive for at least one of the genes investigated. The haemolysin gene (hlyA) was the most isolated gene. The cholera toxin (ctxAB) and non-O1 heat-stable (stn/sto) genes were not detected. Genes were frequently detected at sites influenced by human activities. Thus, identification of V. cholerae VAGs in sediments suggests the possible presence of V. cholerae and identifies sediments of the Apies River as a reservoir for potentially pathogenic V. cholerae with possible public health implications.

Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation. The objective of this work was to evaluate the effect of interannual weather variability on surface water microbial quality. We used the Soil and Water Assessment Tool model to simulate E. coli concentrations in the Little Cove Creek; this is a perennial creek located in an agricultural watershed in south-eastern Pennsylvania. The model performance was evaluated using the US FDA regulatory microbial water quality metrics of geometric mean (GM) and the statistical threshold value (STV). Using the 90-year time series of weather observations, we simulated and randomly sampled the time series of E. coli concentrations. We found that weather conditions of a specific year may strongly affect the evaluation of microbial quality and that the long-term assessment of microbial water quality may be quite different from the evaluation based on short-term observations. The variations in microbial concentrations and water quality metrics were affected by location, wetness of the hydrological years, and seasonality, with 15.7-70.1% of samples exceeding the regulatory threshold. The results of this work demonstrate the value of using modeling to design and evaluate monitoring protocols to assess the microbial quality of water used for produce irrigation.

Release from Streambed to Water Column during Baseflow Periods: A Modeling Study

Streambed sediments can harbor large populations that are released into the water column during high-flow events. Few studies have been conducted on the rates of transfer from streambed sediment to water column in low-flow conditions in natural streams. The aim of this work was to apply the watershed-scale model SWAT (Soil and Water Assessment Tool) to a natural stream to evaluate the need to account for the release from streambed sediments during baseflow periods and to compare the results of simulating such a release by assuming predominantly passive transport, driven by groundwater influx, against simulations assuming predominantly active transport of random or chemotaxis-driven bacteria movement. concentrations in water during baseflow periods were substantially underestimated when release from the streambed was attributed only to streambed sediment resuspension. When considered in addition to the release due to sediment resuspension at high flows, the active and passive release assumptions provided 42 and 4% improvement, respectively, in the RMSE of logarithms of concentrations. Estimated fluxes to water column during the baseflow periods from June to November ranged from 3.3 × 10 colony-forming units (CFU) m d in the game land area to 1.4 × 10 CFU m d in the mixed pasture and cropland. Results demonstrate that release of from streambed sediments during baseflow periods is substantial and that water column concentrations are dependent on not only land management practices but also on in-stream processes.

Enrichment of stream water with fecal indicator organisms during baseflow periods

Fecal indicator organisms (FIOs) are generally believed to be present in surface waters due solely to direct deposition of feces or through transport in runoff. However, emerging evidence points toward hyporheic exchange between sediment pore water and the overlying water column during baseflow periods as a source of FIOs is surface waters. The objective of this work was to (a) propose a mass balance-based technique for estimating changes of FIO concentrations in the same volume of water (or "slug") from the inlet to outlet of stream reaches in baseflow conditions and (b) to use such enumeration to estimate rate of the FIO release to stream water column. Concentrations of Escherichia coli (E. coli) and enterococci were measured in the slug while simultaneously monitoring the movement of a conservative tracer, Br that labeled the slug. Concentrations of E. coli in the slug were significantly larger (P = 0.035, P = 0.001, and P = 0.001, respectively) at the outlet reach in all three replications, while enterococci concentrations were significantly larger in two of three replications (P = 0.001, P < 0.001, and P = 0.602). When estimated without accounting for die-off in water column, FIO net release rates across replications ranged from 36 to 57 cells m^-2 s^-1 and 43 to 87 cells m^-2 s^-1 for E. coli and enterococci, respectively. These release rates were 5 to 20% higher when the die-off in water column was taken into account. No diurnal trends were observed in indicator concentrations. No FIO sources other than bottom sediment have been observed during the baseflow period. FIOs are released into stream water column through hyporheic exchange during baseflow periods.

Modeling fate and transport of fecally-derived microorganisms at the watershed scale: State of the science and future opportunities

Natural waters serve as habitat for a wide range of microorganisms, a proportion of which may be derived from fecal material. A number of watershed models have been developed to understand and predict the fate and transport of fecal microorganisms within complex watersheds, as well as to determine whether microbial water quality standards can be satisfied under site-specific meteorological and/or management conditions. The aim of this review is to highlight and critically evaluate developments in the modeling of microbial water quality of surface waters over the last 10 years and to discuss the future of model development and application at the watershed scale, with a particular focus on fecal indicator organisms (FIOs). In doing so, an agenda of research opportunities is identified to help deliver improvements in the modeling of microbial water quality draining through complex landscape systems. This comprehensive review therefore provides a timely steer to help strengthen future modeling capability of FIOs in surface water environments and provides a useful resource to complement the development of risk management strategies to reduce microbial impairment of freshwater sources.

Mapping of Escherichia coli Sources Connected to Waterways in the Ruamahanga Catchment, New Zealand

Rivers and streams in New Zealand are natural with free access and used by many people for swimming and fishing. However, pastoral farming with free grazing animals is a common land use in New Zealand and faecal microorganisms from them often end up in waterways. These microorganisms can seriously affect human and animal health if ingested. This paper describes spatial modeling using GIS of Escherichia coli sources in a large catchment (350 000 ha), the Ruamahanga. By examining the pathway of water over and through soils, it is possible to determine whether E. coli sources are connected to waterways or not. The map of E. coli sources connected to waterways provides useful context to those setting water quality limits. This approach avoids the complexity of modeling the fate and transport of E. coli in waterways, yet still permits the assessment of catchment-wide mitigation and best management practice. Fencing of waterways would minimize E. coli sources directly defecated to water and would reduce total E. coli sources by approximately 35%. Introduction of dung beetles would minimize sources connected to waterways by overland flow and would reduce total E. coli sources by approximately 35%. Construction of dairy effluent ponds would minimize sources connected to waterways through high bypass flow in soils and would reduce total E. coli sources by approximately 25%.

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).

Predicting fecal indicator organism contamination in Oregon coastal streams

In this study, we used publicly available GIS layers and statistical tree-based modeling (CART and Random Forest) to predict pathogen indicator counts at a regional scale using 88 spatially explicit landscape predictors and 6657 samples from non-estuarine streams in the Oregon Coast Range. A total of 532 frequently sampled sites were parsed down to 93 pathogen sampling sites to control for spatial and temporal biases. This model's 56.5% explanation of variance, was comparable to other regional models, while still including a large number of variables. Analysis showed the most important predictors on bacteria counts to be: forest and natural riparian zones, cattle related activities, and urban land uses. This research confirmed linkages to anthropogenic activities, with the research prediction mapping showing increased bacteria counts in agricultural and urban land use areas and lower counts with more natural riparian conditions.

Long-Term Impacts of Bacteria-Sediment Interactions in Watershed-Scale Microbial Fate and Transport Modeling

Elevated levels of fecal indicator bacteria (FIB) remain the leading cause of surface water-quality impairments in the United States. Under the Clean Water Act, basin-specific total maximum daily load (TMDL) restoration plans are responsible for bringing identified water impairments in compliance with applicable standards. Watershed-scale model predictions of FIB concentrations that facilitate the development of TMDLs are associated with considerable uncertainty. An increasingly cited criticism of existing modeling practice is the common strategy that assumes bacteria behave similarly to "free-phase" contaminants, although many field evidence indicates a nontrivial number of cells preferentially associate with particulates. Few attempts have been made to evaluate the impacts of sediment on the predictions of in-stream FIB concentrations at the watershed scale, with limited observational data available for model development, calibration, and validation. This study evaluates the impacts of bacteria-sediment interactions in a continuous, watershed-scale model widely used in TMDL development. In addition to observed FIB concentrations in the water column, streambed sediment-associated FIB concentrations were available for model calibration. While improved model performance was achieved compared with previous studies, model performance under a "sediment-attached" scenario was essentially equivalent to the simpler "free-phase" scenario. Watershed-specific characteristics (e.g., steep slope, high imperviousness) likely contributed to the dominance of wet-weather pollutant loading in the water column, which may have obscured sediment impacts. As adding a module accounting for bacteria-sediment interactions would increase the model complexity considerably, site evaluation preceding modeling efforts is needed to determine whether the additional model complexity and effort associated with partitioning phases of FIB is sufficiently offset by gains in predictive capacity.

QMRAcatch: Microbial Quality Simulation of Water Resources including Infection Risk Assessment

Given the complex hydrologic dynamics of water catchments and conflicts between nature protection and public water supply, models may help to understand catchment dynamics and evaluate contamination scenarios and may support best environmental practices and water safety management. A catchment model can be an educative tool for investigating water quality and for communication between parties with different interests in the catchment. This article introduces an interactive computational tool, QMRAcatch, that was developed to simulate concentrations in water resources of , a human-associated microbial source tracking (MST) marker, enterovirus, norovirus, , and as target microorganisms and viruses (TMVs). The model domain encompasses a main river with wastewater discharges and a floodplain with a floodplain river. Diffuse agricultural sources of TMVs that discharge into the main river are not included in this stage of development. The floodplain river is fed by the main river and may flood the plain. Discharged TMVs in the river are subject to dilution and temperature-dependent degradation. River travel times are calculated using the Manning-Gauckler-Strickler formula. Fecal deposits from wildlife, birds, and visitors in the floodplain are resuspended in flood water, runoff to the floodplain river, or infiltrate groundwater. Fecal indicator and MST marker data facilitate calibration. Infection risks from exposure to the pathogenic TMVs by swimming or drinking water consumption are calculated, and the required pathogen removal by treatment to meet a health-based quality target can be determined. Applicability of QMRAcatch is demonstrated by calibrating the tool for a study site at the River Danube near Vienna, Austria, using field TMV data, including a sensitivity analysis and evaluation of the model outcomes.

A neighborhood statistics model for predicting stream pathogen indicator levels

Because elevated levels of water-borne Escherichia coli in streams are a leading cause of water quality impairments in the U.S., water-quality managers need tools for predicting aqueous E. coli levels. Presently, E. coli levels may be predicted using complex mechanistic models that have a high degree of unchecked uncertainty or simpler statistical models. To assess spatio-temporal patterns of instream E. coli levels, herein we measured E. coli, a pathogen indicator, at 16 sites (at four different times) within the Squaw Creek watershed, Iowa, and subsequently, the Markov Random Field model was exploited to develop a neighborhood statistics model for predicting instream E. coli levels. Two observed covariates, local water temperature (degrees Celsius) and mean cross-sectional depth (meters), were used as inputs to the model. Predictions of E. coli levels in the water column were compared with independent observational data collected from 16 in-stream locations. The results revealed that spatio-temporal averages of predicted and observed E. coli levels were extremely close. Approximately 66 % of individual predicted E. coli concentrations were within a factor of 2 of the observed values. In only one event, the difference between prediction and observation was beyond one order of magnitude. The mean of all predicted values at 16 locations was approximately 1 % higher than the mean of the observed values. The approach presented here will be useful while assessing instream contaminations such as pathogen/pathogen indicator levels at the watershed scale.

Rainfall-induced runoff from exposed streambed sediments: an important source of water pollution

When surface water levels decline, exposed streambed sediments can be mobilized and washed into the water course when subjected to erosive rainfall. In this study, rainfall simulations were conducted over exposed sediments along stream banks at four distinct locations in an agriculturally dominated river basin with the objective of quantifying the potential for contaminant loading from these often overlooked runoff source areas. At each location, simulations were performed at three different sites. Nitrogen, phosphorus, sediment, fecal indicator bacteria, pathogenic bacteria, and microbial source tracking (MST) markers were examined in both prerainfall sediments and rainfall-induced runoff water. Runoff generation and sediment mobilization occurred quickly (10-150 s) after rainfall initiation. Temporal trends in runoff concentrations were highly variable within and between locations. Total runoff event loads were considered large for many pollutants considered. For instance, the maximum observed total phosphorus runoff load was on the order of 1.5 kg ha. Results also demonstrate that runoff from exposed sediments can be a source of pathogenic bacteria. spp. and spp. were present in runoff from one and three locations, respectively. Ruminant MST markers were also present in runoff from two locations, one of which hosted pasturing cattle with stream access. Overall, this study demonstrated that rainfall-induced runoff from exposed streambed sediments can be an important source of surface water pollution.