Linking watershed modeling and bacterial source tracking to better assess E. coli sources

Current status of microbial source tracking applications in constructed wetlands serving as nature-based solutions for water management and wastewater treatment

Microbial source tracking (MST) has been recognised as an effective tool for determining the origins and sources of faecal contamination in various terrestrial and aquatic ecosystems. Thus, it has been widely applied in environmental DNA (eDNA) surveys to define specific animal- and human-associated faecal eDNA. In this context, identification of and differentiation between anthropogenic and zoogenic faecal pollution origins and sources are pivotal for the evaluation of waterborne microbial contamination transport and the associated human, animal, and environmental health risks. These concerns are particularly pertinent to diverse nature-based solutions (NBS) that are being applied specifically to secure water safety and human and ecosystem well-being, for example, constructed wetlands (CWs) for water and wastewater treatment. The research in this area has undergone a constant evolution, and there is a solid foundation of publications available across the world. Hence, there is an early opportunity to synthesise valuable information and relevant knowledge on this specific topic, which will greatly benefit future work by improving NBS design and performance. By selecting 15 representative research reports published over 20 years, we review the current state of MST technology applied for faecal-associated contamination measures in NBS/CWs throughout the world.

Persistence of E. coli in Streambed Sediment Contaminated with Faeces from Dairy Cows, Geese, and Deer: Legacy Risks to Environment and Health

Legacy stores of faecal pollution in streambed sediments can result in delayed impacts on environmental quality and human health if resuspended into the overlying water column. Different catchment sources of faecal pollution can contribute to a legacy store of microbial pollutants, with size of stores influenced by microbial die-off and faecal accrual rates in the streambed. The aim of this study was to use a mesocosm experiment to characterise the persistence of E. coli derived from faeces of dairy cows, deer, and geese once introduced to streambed sediment under different temperature regimes. The settling rate of solid constituents of faecal material into streambed sediment once delivered into an aquatic environment was also quantified. The persistence patterns of E. coli in streambed sediment were found to vary as a function of faecal source and temperature; die-off of E. coli in sediment contaminated with goose faeces was more rapid than in sediments contaminated with dairy cow or deer faeces. Goose faeces also recorded a more rapid settling rate of faecal particles through the water column relative to dairy cow and deer faeces, suggesting a more efficient delivery of E. coli to streambed sediments associated with this faecal source. Our findings provide new evidence to improve understanding of the potential longer-term risks to both the environment and public health posed by sediments when contaminated with livestock, wildlife, and wildfowl faeces.

Time since faecal deposition influences mobilisation of culturable E. coli and intestinal enterococci from deer, goose and dairy cow faeces

Mobilisation is a term used to describe the supply of a pollutant from its environmental source, e.g., soil or faeces, into a hydrological transfer pathway. The overarching aim of this study was to determine, using a laboratory-based approach, whether faecal indicator bacteria (FIB) are hydrologically mobilised in different quantities from a typical agricultural, wildlife and wildfowl source, namely dairy cattle, red deer and greylag goose faeces. The mobilisation of FIB from fresh and ageing faeces under two contrasting temperatures was determined, with significant differences in the concentrations of both E. coli and intestinal enterococci lost from all faecal sources. FIB mobilisation from these faecal matrices followed the order of dairy cow > goose > deer (greatest to least, expressed as a proportion of the total FIB present). Significant changes in mobilisation rates from faecal sources over time were also recorded and this was influenced by the temperature at which the faecal material had aged over the course of the 12-day study. Characterising how indicators of waterborne pathogens are mobilised in the environment is of fundamental importance to inform models and risk assessments and develop effective strategies for reducing microbial pollution in catchment drainage waters and associated downstream impacts. Our findings add quantitative evidence to support the understanding of FIB mobilisation potential from three important faecal sources in the environment.

Microbial Find, Inform, and Test Model for Identifying Spatially Distributed Contamination Sources: Framework Foundation and Demonstration of Ruminant Bacteroides Abundance in River Sediments

Microbial pollution in rivers poses known ecological and health risks, yet causal and mechanistic linkages to sources remain difficult to establish. Host-associated microbial source tracking (MST) markers help to assess the microbial risks by linking hosts to contamination but do not identify the source locations. Land-use regression (LUR) models have been used to screen the source locations using spatial predictors but could be improved by characterizing transport (i.e., hauling, decay overland, and downstream). We introduce the microbial Find, Inform, and Test (FIT) framework, which expands previous LUR approaches and develops novel spatial predictor models to characterize the transported contributions. We applied FIT to characterize the sources of BoBac, a ruminant Bacteroides MST marker, quantified in riverbed sediment samples from Kewaunee County, Wisconsin. A 1 standard deviation increase in contributions from land-applied manure hauled from animal feeding operations (AFOs) was associated with a 77% (p-value <0.05) increase in the relative abundance of ruminant Bacteroides (BoBac-copies-per-16S-rRNA-copies) in the sediment. This is the first work finding an association between the upstream land-applied manure and the offsite bovine-associated fecal markers. These findings have implications for the sediment as a reservoir for microbial pollution associated with AFOs (e.g., pathogens and antibiotic-resistant bacteria). This framework and application advance statistical analysis in MST and water quality modeling more broadly.

Microbiome Sample Comparison and Search: From Pair-Wise Calculations to Model-Based Matching

A huge quantity of microbiome samples have been accumulated, and more are yet to come from all niches around the globe. With the accumulation of data, there is an urgent need for comparisons and searches of microbiome samples among thousands of millions of samples in a fast and accurate manner. However, it is a very difficult computational challenge to identify similar samples, as well as identify their likely origins, among such a grand pool of samples from all around the world. Currently, several approaches have already been proposed for such a challenge, based on either distance calculation, unsupervised algorithms, or supervised algorithms. These methods have advantages and disadvantages for the different settings of comparisons and searches, and their results are also drastically different. In this review, we systematically compared distance-based, unsupervised, and supervised methods for microbiome sample comparison and search. Firstly, we assessed their accuracy and efficiency, both in theory and in practice. Then we described the scenarios in which one or multiple methods were applicable for sample searches. Thirdly, we provided several applications for microbiome sample comparisons and searches, and provided suggestions on the choice of methods. Finally, we provided several perspectives for the future development of microbiome sample comparison and search, including deep learning technologies for tracking the sources of microbiome samples.

An inverse approach to estimate bacterial loading into an estuary by using field observations and residence time

Pathogen, whose abundance is often measured by the concentration of fecal indicator bacteria, is listed as the top cause of waterbody impairments in the US. An accurate estimation of the bacterial loading from watershed is thus fundamentally important for water quality management. Despite advances in watershed modeling, accurate estimation of bacterial load is still very challenging due to large uncertainties associated with bacterial sources, accumulation, and removal in the watershed. We introduce an inverse method using field-measured bacterial concentrations and numerical model-calculated residence time to estimate the bacterial loading from the drainage basin. In this method, an estuary is divided into multiple segments. Water and bacterial fluxes between neighboring segments are computed from a set of linear equations derived based on mass balance equation and the relationship between residence time and water fluxes. Loading to each segment can then be estimated by combining the computed water fluxes and observed bacterial concentrations. The approach accounts for seasonal and interannual variations in hydrodynamics due to tide, river discharge, and estuarine circulations. The method was applied to Nassawadox Creek, a sub-estuary of Chesapeake Bay, where Fecal Coliform concentrations at 46 stations were continuously monitored. The method is verified by the high consistency between estimated loadings and presumably known input loadings in numerical experiments with either constant or time-varying input loadings. With sparse observational data, the inversely estimated loadings agree well with the loadings from a previously calibrated watershed model, demonstrating the reliability of the method. The inverse approach can be used to cross-check the result of watershed models and assess changes in watershed condition. The method is also readily applicable to other types of materials, such as inorganic nutrients.

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.

Impact of Freeze-Thaw Cycles on Die-Off of E. coli and Intestinal Enterococci in Deer and Dairy Faeces: Implications for Landscape Contamination of Watercourses

Characterising faecal indicator organism (FIO) survival in the environment is important for informing land management and minimising public health risk to downstream water users. However, key gaps in knowledge include understanding how wildlife contribute to catchment-wide FIO sources and how FIO survival is affected by low environmental temperatures. The aim of this study was to quantify E. coli and intestinal enterococci die-off in dairy cow versus red deer faecal sources exposed to repeated freeze–thaw cycles under controlled laboratory conditions. Survival of FIOs in water exposed to freeze–thaw was also investigated to help interpret survival responses. Both E. coli and intestinal enterococci were capable of surviving sub-freezing conditions with the faeces from both animals able to sustain relatively high FIO concentrations, as indicated by modelling, and observations revealing persistence in excess of 11 days and in some cases confirmed beyond 22 days. Die-off responses of deer-derived FIOs in both faeces and water exposed to low temperatures provide much needed information to enable better accounting of the varied catchment sources of faecal pollution and results from this study help constrain the parameterisation of die-off coefficients to better inform more integrated modelling and decision-making for microbial water quality management.

Detection of human fecal pollution in environmental waters using human mitochondrial DNA and correlation with general and human-associated fecal genetic markers

Human mitochondrial DNA (mtDNA) genetic markers are abundant in sewage and highly human-specific, suggesting a great potential for the environmental application as human fecal pollution indicators. Limited data are available on the occurrence and co-occurrence of human mtDNA with fecal bacterial markers in surface waters, and how the abundance of these markers is influenced by rain events. A 1-year sampling study was conducted in a suburban watershed impacted by human sewage contamination to evaluate the performance of a human mtDNA-based marker along with the bacterial genetic markers for human-associated Bacteroidales (BacHum and HF183) and Escherichia coli. Additionally, the human mtDNA-based assay was correlated with rain events and other markers. The mtDNA marker was detected in 92% of samples (n = 140) with a mean concentration of 2.96 log₁₀ copies/100 ml throughout the study period. Human mtDNA was detected with greater abundance than human-associated Bacteroidales that could be attributed to differences in the decay of these markers in the environment. The abundance of all markers was positively correlated with rain events, and human mtDNA abundance was significantly correlated with various bacterial markers. In general, these results should support future risk assessment for impacted watersheds, particularly those affected by human fecal pollution, by evaluating the performance of these markers during rain events.

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.

IPEAT+: A Built-In Optimization and Automatic Calibration Tool of SWAT+

For almost 30 years, the Soil and Water Assessment Tool (SWAT) has been successfully implemented to address issues around various scientific subjects in the world. On the other hand, it has been reaching to the limit of potential flexibility in further development by the current structure. The new generation SWAT, dubbed SWAT+, was released recently with entirely new coding features. SWAT+ is designed to have far more advanced functions and capacities to handle challenging watershed modeling tasks for hydrologic and water quality processes. However, it is still inevitable to conduct model calibration before the SWAT+ model is applied to engineering projects and research programs. The primary goal of this study is to develop an open-source, easy-to-operate automatic calibration tool for SWAT+, dubbed IPEAT+ (Integrated Parameter Estimation and Uncertainty Analysis Tool Plus). There are four major advantages: (i) Open-source code to general users; (ii) compiled and integrated directly with SWAT+ source code as a single executable; (iii) supported by the SWAT developer group; and, (iv) built with efficient optimization technique. The coupling work between IPEAT+ and SWAT+ is fairly simple, which can be conducted by users with minor efforts. IPEAT+ will be regularly updated with the latest SWAT+ revision. If users would like to integrate IPEAT+ with various versions of SWAT+, only few lines in the SWAT+ source code are required to be updated. IPEAT+ is the first automatic calibration tool integrated with SWAT+ source code. Users can take advantage of the tool to pursue more cutting-edge and forward-thinking scientific questions.