Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California

Relationship between Rainfall, Fecal Pollution, Antimicrobial Resistance, and Microbial Diversity in an Urbanized Subtropical Bay

The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.

Urbanized bays are vulnerable to fecal bacterial pollution, and the extent of this pollution, in marine recreational waters, is commonly assessed by quantifying enterococcus concentrations. Recent reports have questioned the utility of enterococci as an indicator of fecal bacterial pollution in subtropical bays impaired by non-point source pollution, and enterococcus data alone cannot identify fecal bacterial sources (i.e., hosts). The purpose of this study was to assess relationships between rainfall, fecal bacterial pollution, antimicrobial resistance, and microbial diversity in an urbanized subtropical bay. Thus, a comprehensive bacterial source tracking (BST) study was conducted using a combination of traditional and modern BST methods. Findings show that rainfall was directly correlated with elevated enterococcus concentrations, including the increased prevalence of Enterococcus faecium, although it was not correlated with an increase in the prevalence of antimicrobial-resistant strains. Rainfall was also correlated with decreased microbial diversity. In contrast, neither rainfall nor enterococcus concentrations were directly correlated with the concentrations of three omnipresent host-associated fecal markers (i.e., human, canine, and gull). Notably, the human fecal marker (HF183) was inversely correlated with enterococcus concentrations, signifying that traditional enterococcus data alone are not an accurate proxy for human fecal waste in urbanized subtropical bays.

IMPORTANCE The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.

Fecal pollution source characterization at non-point source impacted beaches under dry and wet weather conditions

Though Lake Michigan beaches in Chicago are not impacted by stormwater or wastewater outfalls, several of those beaches often exceed USEPA Beach Action Values (BAVs). We investigated the role of microbial source tracking (MST) as a complement to routine beach monitoring at Chicago beaches. In summer 2016, water samples from nine Chicago beaches were analyzed for E. coli by culture and enterococci by qPCR. A total of 195 archived samples were then tested for human (HF183/BacR287, HumM2), canine (DG3, DG37), and avian (GFD) microbial source tracking (MST) markers. Associations between MST and general fecal indicator bacteria (FIB) measures were evaluated and stratified based on wet and dry weather definitions. Among the 195 samples, HF183/BacR287 was quantifiable in 4%, HumM2 in 1%, DG3 in 6%, DG37 in 2%, and GFD in 23%. The one beach with a dog area was far more likely to have DG3 present in the quantifiable range than other beaches. Exceedance of general FIB BAVs increased the odds of human, dog and avian marker detection. MST marker weighted-average fecal scores for DG3 was 2.4 times, DG37 was 2.1 times, and GFD was 1.6 times higher during wet compared to dry weather conditions. HF183/BacR287 weighted-average fecal scores were not associated with precipitation. Associations between FIB BAV exceedance and MST marker detection were generally stronger in wet weather. Incorporating MST testing into routine beach water monitoring can provide information that beach managers can use when developing protection plans for beaches not impacted by point sources.

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

PURPOSE OF REVIEW

Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination.

RECENT FINDINGS

This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.

Residential urban stormwater runoff: A comprehensive profile of microbiome and antibiotic resistance

Non-point stormwater runoff is a major contamination source of receiving waterbodies. Heightened incidence of waterborne disease outbreaks related to recreational use and source water contamination is associated with extreme rainfall events. Such extreme events are predicted to increase in some regions due to climate change. Consequently, municipal separate storm sewer systems (MS4s) conveying pathogens to receiving waters are a growing public health concern. In addition, the spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria in various environmental matrices, including urban runoff, is an emerging threat. The resistome and microbiota profile of MS4 discharges has yet to be fully characterized. To address this knowledge gap, we first analyzed the relationship between rainfall depth and intensity and E. coli densities (fecal indicator) in stormwater from four MS4 outflows in Columbus, Ohio, USA during the spring and summer of 2017. Microbial source tracking (MST) was conducted to examine major fecal contamination sources in the study sewersheds. A subset of samples was analyzed for microbial and resistome profiles using a metagenomic approach. The results showed a significant positive relationship between outflow E. coli density and rainfall intensity. MST results indicate prevalent fecal contamination from ruminant populations in the study sites (91% positive among the samples tested). Protobacteria and Actinobacteria were two dominant bacteria at a phylum level. A diverse array of ARGs and potentially pathogenic bacteria (e.g. Salmonella enterica Typhimurium), fungi (e.g. Scedosporium apiospermum), and protists (e.g. Acanthamoeba palestinensis) were found in urban stormwater outflows that discharge into adjacent streams. The most prevalent ARGs among samples were β-lactam resistance genes and the most predominant virulence genes within bacterial community were related with Staphylococcus aureus. A comprehensive contamination profile indicates a need for sustainable strategies to manage urban stormwater runoff amid increasingly intense rainfall events to protect public and environmental health.

Surf zone microbiological water quality following emergency beach nourishment using sediments from a catastrophic debris flow

Urban disaster response requires disposal of complex wastes. This study regards a case wherein high intensity rainfall fell over a remote mountainous area previously burned by wildfire, generating debris flows that devastated a downstream town. Sanitary sewers and homes with septic systems were damaged, releasing human waste into the debris flow field. Contaminated sediments, with their high fecal indicator bacteria (FIB) concentrations, were cleared from public rights-of-way and creek channels by local authorities, then disposed onto distant Goleta Beach for beach nourishment, causing immediate surf zone microbiological water quality exceedances. To determine potential public health threats, disposed sediments and surf zone waters were sampled and analyzed-relative to reference samples of mountain soil and raw sewage-for FIB, pathogens, human (HF183) and other host- (Gull2 TaqMan, and DogBact) associated DNA-based fecal markers, and bacterial community 16S rRNA gene sequences. Approximately 20% of disposed sediment samples contained the HF183 marker; sequencing suggested that all samples were contaminated by sewage. In an initial sediment disposal period, surf zone waters harbored intestinal bacterial sequences that were shared with disposed sediments and sewage. Yet surf zone bacterial communities returned to mostly marine clades within weeks. Taken together, multiple conventional and DNA-based analyses informed this forensic assessment of human waste contamination. In the future, similar analyses could be used earlier in disaster response to guide sediment disposal decisions towards continuously protecting beachgoer health.

Utility of QMRA to compare health risks associated with alternative urban sewer overflow management strategies

Wet weather sewer overflows pose potential short-term public health risks. With increasing populations, aging infrastructure and climate change, utilities are challenged with managing sewerage infrastructure to provide optimum outcomes. This study compared how modelled public health risk profiles could change under alternative sewer overflow management strategies during 12 and 24-month rainfall-runoff events. Specifically, existing conditions were compared with both a 'business-as-usual' (BAU) sewer upgrade and a more holistic 'effects-based planning' (EBP) approach based on pumped wet weather sewage overflows directed to a local receiving waterway. Options were compared based on their efficacy to reduce manhole overflows, recreational waterway guideline exceedances and downstream recreational waterway health risks estimated through a screening-level Quantitative Microbial Risk Assessment (QMRA). Results indicated that the two management strategies would be equally effective in reducing the frequency, duration and volume of manhole sewer overflows, eliminating them in the 12-month scenarios and reducing them from >5000 m³ for the 24-month baseline scenario, to 23 and 35 m³ for BAU and EBP, respectively. Baseline, BAU and EBP scenarios produced similar hours of enterococci guideline exceedances, ranging from 1 to 4 h difference. The QMRA produced similar health risk profiles for downstream recreational waterway users for all design events, suggesting that sewer overflows are not the primary driver of public health risks during and immediately following high rainfall events. As such, QMRA provided evidence that an EBP strategy may be used to manage wet weather sewer overflows in lieu of an expensive BAU upgrade, without exacerbating the public health of downstream waterway users. Further investigation of the broader environmental health impacts of implementing this type of innovative approach is warranted. Nonetheless, this work highlights the value of integrating QMRA with other modelling approaches to guide and inform sewer overflow management.

Verification of Bacteroidales 16S rRNA markers as a complementary tool for detecting swine fecal pollution in the Yangtze Delta

To correctly assess and properly manage the public health risks associated with exposure to contaminated water, it is necessary to identify the source of fecal pollution in a watershed. In this study, we evaluated the efficacy of our two previously developed real time-quantitative PCR (qPCR) assays for the detection of swine-associated Bacteroidales genetic markers (gene 1-38, gene 3-53) in the Yangtze Delta watershed of southeastern China. The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy (92.5%, 91.7% conditional probability, respectively) in detecting Bacteroidales spp. in water samples. According to binary logistic regression (BLR), these two swine-associated markers were well correlated (P < 0.05) with fecal indicators (Escherichia coli and Enterococci spp.) and zoonotic pathogens (E. coli O157: H7, Salmonella spp. and Campylobacter spp.) in water samples. In contrast, concentrations of conventional fecal indicator bacteria (FIB) were not correlated with zoonotic pathogens, suggesting that they are noneffective at detecting fecal pollution events. Collectively, the results obtained in this study demonstrated that a swine-targeted qPCR assay based on two Bacteroidales genes markers (gene 1-38, gene 3-53) could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.

The pollution conveyed by urban runoff: A review of sources

Urban stormwater and snowmelt pollution contributes significantly to the deterioration of surface waters quality in many locations. Consequently, the sources of such pollution have been studied for the past 50 years, with the vehicular transportation sector and the atmospheric deposition identified early as the major pollution sources. In search for mitigation of this pollution, source controls, besides other measures, were recognised as effective pollution mitigation tools, whose successful implementation requires a good knowledge of pollution sources. Even though great research efforts have been exerted to document specific sources of urban runoff pollution, or specific groups of pollutants present in urban runoff, a comprehensive overview of all known contributing sources is still missing. This review contributes to closing this gap by compiling findings of previous research and critically synthesizing the current knowledge of various stormwater pollution sources. As the emphasis is placed on the sources, the related issues of implications for urban surface water quality and possible source controls for individual sources are touched upon just briefly, where required. The review showed that the atmospheric deposition, vehicular transportation-related activities and metallic building envelopes continue to be among the major pollution sources, which have been studied in a far greater detail than other sources. Furthermore, it was noted that because of the rapid advances in clean manufacturing and pollution control technologies, a large part of the body of data on stormwater quality available in the literature should be considered as historical data, which may no longer describe well the current conditions. Progressing historical data obsolescence, combined with continuing releases of new materials and chemicals, and, in some cases of new substances of potential concern, into the environment, suggests that the identification of important stormwater runoff/snowmelt pollution sources, and the associated pollutants, has been and will remain to be a work in progress.

Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration

The quantification of pathogens is important for assessing water safety and preventing disease outbreaks. Culture-independent approaches, such as quantitative PCR (qPCR) and digital PCR (dPCR), are useful techniques for quantifying pathogens in water samples. However, since pathogens are usually present at low concentrations in water, it is necessary to concentrate microbial cells before extracting their DNA. Many existing microbial concentration methods are inefficient or take a long time to perform. In this study, we applied a coagulation and foam separation method to concentrate environmental water samples of between 1000 and 5000 mL to 100 μL of DNA (i.e., a 1-5 × 10⁴-fold concentration). The concentration process took <1 h. The DNA samples were then used to quantify various target pathogens using dPCR. One gene, the Shiga toxin gene (stx₂) of Shiga toxin-producing Escherichia coli, was detected at 32 copies/100 mL in a river water sample. The coagulation and foam concentration method followed by dPCR reported herein is a fast, sensitive, and reliable method to quantify pathogen genes in environmental water samples.

Sewage-associated marker genes illustrate the impact of wet weather overflows and dry weather leakage in urban estuarine waters of Sydney, Australia

This study investigates the impact of wet weather overflows (WWOs) at three estuarine locations in Sydney, NSW, Australia. WWOs can occur when infiltration of stormwater leads to an excess volume of flow within the sewerage system, resulting in the release of diluted sewage into the environment. Sewage contamination poses a risk to human health due to the presence of pathogens. The magnitude of sewage contamination was monitored using established and novel sewage-associated marker genes, Bacteroides HF183, pepper mild mottle virus (PMMoV), crAssphage CPQ_056, Lachnospiraceae (Lachno3) marker genes along with culturable fecal indicator bacteria (FIB) Escherichia coli (E. coli) and enterococci. Water samples were collected at two water depths (0.5 m below the water surface and 1 m above the bottom surface) during one dry weather and two storm events. Analysis of sewage-associated marker genes showed greater (i.e., 3-5 orders of magnitude) concentrations in water samples collected during the storm events compared to dry weather event. Water samples were also analysed for four animal feces-associated marker genes targeting avian (GFD), dog (BacCan-UCD), cow (cowM2) and horse (HoF597) species to determine the extent of animal fecal contamination. Among the four marker genes, cowM2 and HoF597 could not be detected, while GFD marker gene was consistently present and BacCan-UCD was occasionally detected. Overall results suggested that after rainfall, untreated sewage from WWOs was present at sampling locations. In addition, microbial source tracking (MST) monitoring was able to distinguish the presence of a leaking sewer impacting on the recreational area during dry weather condition. This study demonstrated the capability of the MST monitoring approach to understand sources (sewage or animal) of fecal contamination. This capability will greatly enhance management decisions assisting in the prioritisation of remediation efforts of the sewerage system to improve estuarine bathing water quality and diminish human health risk.

Landscape, Water Quality, and Weather Factors Associated With an Increased Likelihood of Foodborne Pathogen Contamination of New York Streams Used to Source Water for Produce Production

There is a need for science-based tools to (i) help manage microbial produce safety hazards associated with preharvest surface water use, and (ii) facilitate comanagement of agroecosystems for competing stakeholder aims. To develop these tools an improved understanding of foodborne pathogen ecology in freshwater systems is needed. The purpose of this study was to identify (i) sources of potential food safety hazards, and (ii) combinations of factors associated with an increased likelihood of pathogen contamination of agricultural water Sixty-eight streams were sampled between April and October 2018 (196 samples). At each sampling event separate 10-L grab samples (GS) were collected and tested for Listeria, Salmonella, and the stx and eaeA genes. A 1-L GS was also collected and used for Escherichia coli enumeration and detection of four host-associated fecal source-tracking markers (FST). Regression analysis was used to identify individual factors that were significantly associated with pathogen detection. We found that eaeA-stx codetection [Odds Ratio (OR) = 4.2; 95% Confidence Interval (CI) = 1.3, 13.4] and Salmonella isolation (OR = 1.8; CI = 0.9, 3.5) were strongly associated with detection of ruminant and human FST markers, respectively, while Listeria spp. (excluding Listeria monocytogenes) was negatively associated with log10 E. coli levels (OR = 0.50; CI = 0.26, 0.96). L. monocytogenes isolation was not associated with the detection of any fecal indicators. This observation supports the current understanding that, unlike enteric pathogens, Listeria is not fecally-associated and instead originates from other environmental sources. Separately, conditional inference trees were used to identify scenarios associated with an elevated or reduced risk of pathogen contamination. Interestingly, while the likelihood of isolating L. monocytogenes appears to be driven by complex interactions between environmental factors, the likelihood of Salmonella isolation and eaeA-stx codetection were driven by physicochemical water quality (e.g., dissolved oxygen) and temperature, respectively. Overall, these models identify environmental conditions associated with an enhanced risk of pathogen presence in agricultural water (e.g., rain events were associated with L. monocytogenes isolation from samples collected downstream of dairy farms; P = 0.002). The information presented here will enable growers to comanage their operations to mitigate the produce safety risks associated with preharvest surface water use.

Developing Unique Nontarget High-Resolution Mass Spectrometry Signatures to Track Contaminant Sources in Urban Waters

Diffuse pollution in urban receiving waters often adversely impacts both humans and ecosystems. Identifying such pollution sources is challenging and limits the effectiveness of management actions intended to reduce risk. Here, we evaluated the use of nontarget analysis via high-resolution mass spectrometry (HRMS) to develop chemical fingerprints/signatures for source tracking. Specifically, we applied nontarget HRMS to characterize and differentiate two urban chemical sources: roadway runoff and wastewater influent. We isolated 112 and 598 nontarget compounds (both known and unidentified chemicals) that co-occurred in all roadway runoff and wastewater influent samples, respectively, and were unique relative to other sampled sources. For example, methamphetamine, often considered wastewater derived, was detected in all samples, implying that individual wastewater indicators may lack sufficient specificity in urban receiving waters impacted by multiple sources. Hierarchical cluster analysis differentiated source types, and normalized abundance profiling prioritized nontarget compounds with consistent relative abundance patterns across field sites for a given source. Hexa(methoxymethyl)melamine, 1,3-diphenylguanidine, and polyethylene glycols co-occurred in roadway runoff across geographic areas and traffic intensities, supporting continued development of a universal roadway runoff fingerprint based on ubiquitous compounds. This study provides a proof-of-concept for isolating nontarget source fingerprints to track diffuse contamination in urban receiving waters.

Biotic concerns in generating molecular diagnosis matrixes for 4 avian viruses with emphasis on Marek's disease virus

The great advance in the field of diagnosis of avian viruses is reflecting the highly sophisticated molecular assays of the human and general virology in providing highly sensitive and fast methods of diagnosis. The present review will discuss the biotic factors and the complexities that became evident with the evolution of the novel molecular diagnostic assays with emphasis on 4 avian viruses, chicken anemia, infectious laryngotracheitis, turkey meningoencephalitis, but mainly on Marek's disease virus. To create a biologically meaningful diagnosis, attention should be dedicated to various biotic factors and not only of the diagnostic assay. Included among the important factors are, (a) the sample examined and the sampling strategy, (b) the outcomes of the pathogen amplification ex vivo, (c) the sampling time and its reflection on the disease diagnosis, (d) the impact of simultaneous multiple virus-infections regarding the ability to demonstrate all pathogens and inter- and intra-interactions between the pathogens. A concerted consideration of the relevant factors and the use of advanced molecular diagnostic assay would yield biologically significant diagnosis in real-time that would beneficiate the poultry industry.

A review on microbial contaminants in stormwater runoff and outfalls: Potential health risks and mitigation strategies

Demands on global water supplies are increasing in response to the need to provide more food, water, and energy for a rapidly growing population. These water stressors are exacerbated by climate change, as well as the growth and urbanisation of industry and commerce. Consequently, urban water authorities around the globe are exploring alternative water sources to meet ever-increasing demands. These alternative sources are primarily treated sewage, stormwater, and groundwater. Stormwater including roof-harvested rainwater has been considered as an alternative water source for both potable and non-potable uses. One of the most significant issues concerning alternative water reuse is the public health risk associated with chemical and microbial contaminants. Several studies to date have quantified fecal indicators and pathogens in stormwater. Microbial source tracking (MST) approaches have also been used to determine the sources of fecal contamination in stormwater and receiving waters. This review paper summarizes occurrence and concentrations of fecal indicators, pathogens, and MST marker genes in urban stormwater. A section of the review highlights the removal of fecal indicators and pathogens through water sensitive urban design (WSUD) or Best Management Practices (BMPs). We also discuss approaches for assessing and mitigating health risks associated with stormwater, including a summary of existing quantitative microbial risk assessment (QMRA) models for potable and non-potable reuse of stormwater. Finally, the most critical research gaps are identified for formulating risk management strategies.

Synergy between quantitative microbial source tracking (qMST) and quantitative microbial risk assessment (QMRA): A review and prospectus

The use of microbial source tracking (MST) marker genes has grown in recent years due to the need to attribute point and non-point fecal contamination to specific sources. Quantitative microbial risk assessment (QMRA) is a modeling approach used to estimate health risks from exposure to feces-contaminated water and associated pathogens. A combination of these approaches [quantitative MST (qMST) and QMRA] can provide additional pathogen-related information for prioritizing and addressing health risks, compared to reliance on conventional fecal indicator bacteria (FIB). To inform expansion of this approach, a review of published qMST-QMRA studies was conducted to summarize the state of the science and to identify research needs. The reviewed studies primarily aimed to identify what levels of MST marker genes in hypothetical recreational waterbodies would exceed the United States Environmental Protection Agency (USEPA) risk benchmarks for primary contact recreators. The QMRA models calculated relationships between MST marker gene(s) and reference pathogens based on published data in the literature. The development of a robust, accurate relationship was identified as an urgent research gap for qMST-QMRA. This metric requires additional knowledge to quantify the relationship between MST marker genes and the degree of variability in decay of pathogens as a dynamic function of environmental conditions and combinations of fecal sources at multiple spatial and temporal scales. Improved characterization of host shedding rates of host-associated microorganisms (i.e., MST marker genes), as well as fate and transport of these microorganisms and their nucleic acids, would facilitate expansion of this approach to other exposure pathways. Incorporation of information regarding the recovery efficiency, and host-specificity of MST marker genes into QMRA model parameters, and the sensitivity analysis, would greatly improve risk management and site-specific water monitoring criteria.

Microbial Source Tracking Analysis Using Viral Indicators in Santa Lucía and Uruguay Rivers, Uruguay

The aim of this study was to determine the origin (human, bovine or porcine) and the concentration of the fecal sources of contamination in waters from Santa Lucía basin and Uruguay River in Uruguay by using host-specific viral markers (adenoviruses and polyomaviruses) as microbial source tracking (MST). Between June 2015 and May 2016, monthly collections of surface water samples were performed in six sites in Santa Lucía basin and four sites in Uruguay River (n = 120 samples). Viral concentration was carried out using an absorption-elution method. Detection and quantification of human and porcine adenovirus (HAdV and PAdV, respectively) and human and bovine polyomavirus (HPyV and BoPyV, respectively) were performed by quantitative PCR (qPCR). To evaluate the infectivity of circulating HAdV, an integrated cell culture-qPCR (ICC-qPCR) was used. A logistic regression analysis was carried out to estimate the influence of environmental variables on the virus presence in surface waters. Overall, HAdV was the prevalent (18%; 21/120) followed by BoPyV (11%; 13/120) and HPyV (3%; 3/120), whereas PAdV was not detected in this study. The mean concentration ranged from 1.5 × 10⁴ genomic copies/L (gc/L) for HAdV to 1.8 × 10² gc/L for HPyV. Infective HAdVs were observed in two out of ten analyzed samples. A significant effect of environmental temperature (p = 0.001) and river (p = 0.012) on the presence of human viruses was found. These results suggest that fecal contamination could affect the water quality of these rivers, showing deficiencies in the procedure of sewage discharge from regional cities, livestock and dairy farms.

Enhanced insights from human and animal host-associated molecular marker genes in a freshwater lake receiving wet weather overflows

This study investigated the magnitude of wet weather overflow (WWO)-driven sewage pollution in an urban lake (Lake Parramatta) located in Sydney, New South Wales, Australia. Water samples were collected during a dry weather period and after two storm events, and tested for a range of novel and established sewage- [Bacteroides HF183, crAssphage CPQ_056 and pepper mild mottle virus (PMMoV)] and animal feces-associated (Bacteroides BacCan-UCD, cowM2 and Helicobacter spp. associated GFD) microbial source tracking marker genes along with the enumeration of culturable fecal indicator bacteria (FIB), namely Escherichia coli (E. coli) and Enterococcus spp. The magnitude of general and source-specific fecal pollution was low in water samples collected during dry weather compared to storm events. The levels of HF183, crAssphage and PMMoV in water samples collected during storm events were as high as 6.39, 6.33 and 5.27 log10 GC/L of water, respectively. Moderate to strong positive correlations were observed among the quantitative occurrence of sewage-associated marker genes. The concentrations of HF183 and PMMoV in most storm water samples exceeded the risk benchmark threshold values established in the literature for primary contact recreators. None of the samples tested was positive for the cowM2 (cow) marker gene, while BacCan-UCD (dog) and GFD (avian) animal-associated markers were sporadically detected in water samples collected from both dry weather and storm events. Based on the results, the ongoing advice that swimming should be avoided for several days after storm events appears appropriate. Further research to determine the decay rates of sewage-associated marker genes in relation to each other and enteric viruses would help refine current advice. Microbial source tracking approaches employed in this study provided insights into sources of contamination over currently used FIB.

A Quantity–Quality Model to Assess the Effects of Source Control Stormwater Management on Hydrology and Water Quality at the Catchment Scale

The vast development of urban areas has resulted in the increase of stormwater peak runoff and volume. Water quality has also been adversely affected. The best management practices (BMPs) and low impact development (LID) techniques could be applied to urban areas to mitigate these effects. A quantity–quality model was developed to simulate LID practices at the catchment scale using the US Environmental Protection Agency Storm Water Management Model (US EPA SWMM). The purpose of the study was to investigate the impacts of LID techniques on hydrology and water quality. The study was performed in BUNUS catchment in Kuala Lumpur, Malaysia. This study applied vegetated swale and rain garden to assess the model performance at a catchment scale using real field data. The selected LIDs occupied 7% of each subcatchment (of which 40% was swale and 30% was rain garden). The LID removal efficiency was up to 40% and 62% for TN and TSS, respectively. The peak runoff reduction was up to 27% for the rainfall of up to 70 mm, and up to 19% for the rainfall of between 70 and 90 mm, respectively. For the longer storm events of higher than 90 mm the results were not as satisfactory as expected. The model was more effective in peak runoff reduction during the shorter rainfall events. As for the water quality, it was satisfactory in all selected rainfall scenarios.

Testing of new stormwater pollution build-up algorithms informed by a genetic programming approach

Pollution build-up and wash-off processes are often included in urban stormwater quality models. However, these models are often unreliable and have poor performance at large scales and in complicated catchments. This study tried to improve stormwater quality models by adopting the genetic programming (GP) approach to generate new build-up algorithms for three different pollutants (total suspend solids - TSS, total phosphorus - TP and total nitrogen - TN). This was followed by testing of the new models (also traditional build-up and wash-off models as benchmark) using data collected from different catchments in Australia and the USA. The GP approach informed new sets of build-up algorithms with the inclusion of not just the typical antecedent dry weather period (ADWP), but also other less 'traditional' variables - previous rainfall depth for TSS and maximum air temperatures for TP and TN simulation. The traditional models had relatively poor performance (Nash-Sutcliffe coefficient, E < 0.0), except for TP at Gilby Road (GR) (E = 0.21 in calibration and 0.43 in validation). Improved performance was observed using the models with new build-up algorithms informed by GP. Taking TP at GR for example, the best performing model had E of 0.46 in calibration and 0.54 in validation. The best performing models for TSS, TP, and TN are often different, suggesting that specific models shall be used for different pollutants. Insights into further improvements possible for stormwater quality models were given. It is recommended that in addition to the typical build-up and wash-off process, new generations of stormwater quality models should be able to account for the non-conventional pollutant sources (e.g. cross-connections, septic tank leakage, illegal discharges) through stochastic approaches. Emission inventories with information like intensity-frequency-duration (IFD) of pollutant loads from each type of non-conventional source are suggested to be built for stochastic modelling.

Atmospheric rivers impact California's coastal water quality via extreme precipitation

Precipitation in California is projected to become more volatile: less frequent but more extreme as global warming pushes midlatitude frontal cyclones further poleward while bolstering the atmospheric rivers (ARs), which tend to produce the region's extreme rainfall. Pollutant accumulation and delivery to coastal waters can be expected to increase, as lengthening dry spells will be increasingly punctuated by more extreme precipitation events. Coastal pollution exposes human populations to high levels of fecal bacteria and associated pathogens, which can cause a variety of health impacts. Consequently, studying the impact of atmospheric rivers as the mechanism generating pulses of water pollution in coastal areas is relevant for public health and in the context of climate change. We aimed to quantify the links between precipitation events and water quality in order to explore meteorological causes as first steps toward effective early warning systems for the benefit of population health in California and beyond. We used historical gridded daily precipitation and weekly multiple fecal bacteria indicators at ~500 monitoring locations in California's coastal waters to identify weekly associations between precipitation and water quality during 2003-09 using canonical correlation analysis to account for the nested/clustered nature of longitudinal data. We then quantified, using a recently published catalog of atmospheric rivers, the proportion of coastal pollution events attributable to ARs. Association between precipitation and fecal bacteria was strongest in Southern California. Over two-thirds of coastal water pollution spikes exceeding one standard deviation were associated with ARs. This work highlights the importance of skillful AR landfall predictions in reducing vulnerability to extreme weather improving resilience of human populations in a varying and changing climate. Quantifying the impacts of ARs on waterborne diseases is important for planning effective preventive strategies for public health.

Biotreatment technologies for stormwater harvesting: critical perspectives

Biotreatment technologies offer many advantages for passive stormwater treatment before harvesting, but performance can be variable and sensitive to system design, construction, operation and maintenance. While there is substantial research underpinning pollutant removal, hydraulic function, internal processes and optimal design, specific focus upon stormwater harvesting is relatively limited. Recent advances in system design include testing media amendments for targeted pollutant removal, enhanced pathogen removal using antimicrobial plants, and broadening technology application. However, the production of reliable fit-for-purpose water requires the development of robust validation methodologies to meet public safety expectations. While foundation studies exist, more needs to be done to extend the validation framework, monitor and control system performance and operation in real-time, and apply standards and regulatory checks.

Quantification of Microbial Source Tracking and Pathogenic Bacterial Markers in Water and Sediments of Tiaoxi River (Taihu Watershed)

Taihu Lake is one of the largest freshwater lakes in China, serving as an important source of drinking water; >60% of source water to this lake is provided by the Tiaoxi River. This river faces serious fecal contamination issues, and therefore, a comprehensive investigation to identify the sources of fecal contamination was carried out and is presented here. The performance of existing universal (BacUni and GenBac), human (HF183-Taqman, HF183-SYBR, BacHum, and Hum2), swine (Pig-2-Bac), ruminant (BacCow), and avian (AV4143 and GFD) associated microbial source tracking (MST) markers was evaluated prior to their application in this region. The specificity and sensitivity results indicated that BacUni, HF183-TaqMan, Pig-2-Bac, and GFD assays are the most suitable in identifying human and animal fecal contamination. Therefore, these markers along with marker genes specific to selected bacterial pathogens were quantified in water and sediment samples of the Tiaoxi River, collected from 15 locations over three seasons during 2014 and 2015. Total/universal Bacteroidales markers were detected in all water and sediment samples (mean concentration 6.22 log10 gene copies/100 ml and 6.11 log10 gene copies/gram, respectively), however, the detection of host-associated MST markers varied. Human and avian markers were the most frequently detected in water samples (97 and 89%, respectively), whereas in sediment samples, only human-associated markers were detected more often (86%) than swine (64%) and avian (8.8%) markers. The results indicate that several locations in the Tiaoxi River are heavily polluted by fecal contamination and this correlated well with land use patterns. Among the five bacterial pathogens tested, Shigella spp. and Campylobacter jejuni were the most frequently detected pathogens in water (60% and 62%, respectively) and sediment samples (91% and 53%, respectively). Shiga toxin-producing Escherichia coli (STEC) and pathogenic Leptospira spp. were less frequently detected in water samples (55% and 33%, respectively) and sediment samples (51% and 13%, respectively), whereas E. coli O157:H7 was only detected in sediment samples (11%). Overall, the higher prevalence and concentrations of Campylobacter jejuni, Shigella spp., and STEC, along with the MST marker detection at a number of locations in the Tiaoxi River, indicates poor water quality and a significant human health risk associated with this watercourse. GRAPHICAL ABSTRACTTracking fecal contamination and pathogens in watersheds using molecular methods.

Critical issues in application of molecular methods to environmental virology

Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.

Developing a framework for stormwater management: leveraging ancillary benefits from urban greenspace

Managing stormwater and wastewater has been a priority for cities for millennia, but has become increasingly complicated as urban areas grow and develop. Since the mid-1800s, cites often relied on an integrated system of underground pipes, pumps, and other built infrastructure (termed gray infrastructure) to convey stormwater away from developed areas. Unfortunately, this gray infrastructure is aging and often exceeds its designed capacity. In an effort to alleviate issues related to excess stormwater, many urban areas across the United States are interested in using green infrastructure as a stopgap or supplement to inadequate gray infrastructure. Green infrastructure and other greenspace promote interception and/or infiltration of stormwater by using the natural hydrologic properties of soil and vegetation. Furthermore, there are numerous ancillary benefits, in addition to stormwater benefits, that make the use of greenspace desirable. Collectively, these ecosystem services can benefit multiple aspects of a community by providing benefits in a targeted manner. In this paper, we present a framework for balancing stormwater management against ancillary benefits of urban greenspace. The framework is structured around the Millennium Ecosystem Assessment ecosystem service categories: provisioning, cultural, regulatory, and supporting services. The purpose is to help communities better manage their systems by 1) allowing stakeholders to prioritize and address their needs and concerns within a community, and 2) maximize the ecosystem service benefits received from urban greenspace.

Factors affecting microbial and physico-chemical pollutants in stormwater in a typical Chinese urban catchment

An understanding of microbial pollution characteristics is needed for stormwater reuse and development of microorganism simulations in urban stormwater. This study investigated the discharge characteristics of faecal indicator bacteria (faecal coliforms) in urban runoff by field sampling both the underlying surfaces and the stormwater pipe outlet. Faecal coliform contamination in urban runoff was found to be frequent, and the highest instantaneous concentration reached 2.42 × 106 MPN/100 ml. Faecal coliforms did not show a consistent first flush effect amongst the different surfaces sampled, and this was exacerbated under rainfall events with high intensity. PROMETHEE (Preference Ranking Organization Method for Enrichment Evaluation) and GAIA (Geometrical Analysis for Interactive Aid) analyses were further applied to explore the ranking of pollutants, the relationship among the pollutants, and the factors affecting the contamination in cases of multiple underlying surfaces, multiple pollutants and rainfall events. For the pollutants of suspended solids (SS), total phosphorus (TP) and chemical oxygen demand (COD), the road sample contamination was significantly higher than on the roof surfaces. No such trend in ranking of faecal coliforms was observed. Rainfall depth and intensity were found to have a significant influence on stormwater contamination by physico-chemical pollutants, while having a somewhat smaller influence on faecal coliform contamination. Faecal coliform contamination is closely associated with the index related to the antecedent dry period. The average temperature and average relative humidity also showed a positive relationship with faecal coliform contamination. The effects of antecedent dry period duration on contamination of physico-chemical pollutants and faecal coliform are completely opposite. Antecedent dry period duration was positively related to the contamination of physico-chemical pollutants, but negatively related to faecal coliform contamination. Therefore, three variables, i.e., antecedent dry period duration, average temperature and average relative humidity, might be used to model the survival/die-off of faecal coliform during the antecedent dry period.

Novel crAssphage marker genes ascertain sewage pollution in a recreational lake receiving urban stormwater runoff

Considerable efforts have been made in recent years in developing novel marker genes for fecal pollution tracking in environmental waters. CrAssphage are recently discovered DNA bacteriophage that are highly abundant in human feces and untreated sewage. In this study, we evaluated the host-sensitivity and -specificity of the newly designed crAssphage qPCR assays (Stachler et al., 2017) CPQ_056 and CPQ_064 (i.e., marker genes) in fecal samples collected from various human and several animal host groups in Australia. We also investigated the utility of these marker genes to detect sewage pollution in an urban recreational lake (i.e., Lake Parramatta) in Sydney, NSW. The mean concentrations of CPQ_056 and CPQ_064 marker genes in untreated sewage were 9.43 ± 0.14 log₁₀ GC/L and 8.91 ± 0.17 log₁₀ GC/L, respectively, 2 to 3 orders of magnitude higher than other sewage-associated viruses used in microbial source tracking studies. Among 177 animal fecal samples tested from 11 species, the host-specificity values for CPQ_056 and CPQ_064 marker genes were 0.95 and 0.93, respectively. Limited cross-reactivity was observed with cat fecal and cattle wastewater samples. Abundance of crAssphage markers were monitored in an urban lake that receives stormwater runoff. The concentrations of both markers were higher (CPQ_056 ranging from 3.40 to 6.04 log₁₀ GC/L and CPQ_064 ranging from 2.90 to 5.47 log₁₀ GC/L) in 20 of 20 (for CPQ_056) and 18 of 20 (for CPQ_064) samples collected after storm events with gauged sewer overflows compared to dry weather event (10 of 10 samples were qPCR negative for the CPQ_056 and 8 of 10 were negative for the CPQ_064 marker genes) suggesting sewage pollution was transported by urban stormwater runoff to Lake Parramatta. The results of the study may provide context for management of sewage pollution from gauged overflow points of the sewerage system in the catchment.

Patterns of Host-Associated Fecal Indicators Driven by Hydrology, Precipitation, and Land Use Attributes in Great Lakes Watersheds

Fecal contamination from sewage and agricultural runoff is a pervasive problem in Great Lakes watersheds. Most work examining fecal pollution loads relies on discrete samples of fecal indicators and modeling land use. In this study, we made empirical measurements of human and ruminant-associated fecal indicator bacteria and combined these with hydrological measurements in eight watersheds ranging from predominantly forested to highly urbanized. Flow composited river samples were collected over low-flow ( n = 89) and rainfall or snowmelt runoff events ( n = 130). Approximately 90% of samples had evidence of human fecal pollution, with highest loads from urban watersheds. Ruminant indicators were found in ∼60-100% of runoff-event samples in agricultural watersheds, with concentrations and loads related to cattle density. Rain depth, season, agricultural tile drainage, and human or cattle density explained variability in daily flux of human or ruminant indicators. Mapping host-associated indicator loads to watershed discharge points sheds light on the type, level, and possible health risk from fecal pollution entering the Great Lakes and can inform total maximum daily load implementation and other management practices to target specific fecal pollution sources.

Microbial Source Tracking Using Quantitative and Digital PCR To Identify Sources of Fecal Contamination in Stormwater, River Water, and Beach Water in a Great Lakes Area of Concern

Areas of concern (AOCs) around the Great Lakes are characterized by historic and ongoing problems with microbial water quality, leading to beneficial use impairments (BUIs) such as beach postings and closures. In this study, we assessed river and beach sites within the Rouge River watershed, associated stormwater outfalls, and at Rouge Beach. The concentrations of Escherichia coli as well as human- and gull-specific qPCR microbial source tracking (MST) markers were assessed at all sites. A preliminary comparison of digital PCR (dPCR) methodologies for both MST markers was conducted regarding sensitivity and specificity. Within the watershed, the outfalls were found to be a prominent source of human fecal contamination, with two outfalls particularly affected by sewage cross-connections. However, the occurrence of human fecal contamination along Rouge Beach and in the lower portions of the watershed was largely dependent on rain events. Gull fecal contamination was the predominant source of contamination at the beach, particularly during dry weather. The multiplex human/gull dPCR methodology used in this study tended to be more sensitive than the individual quantitative PCR (qPCR) assays, with only a slight decrease in specificity. Both dPCR and qPCR methodologies identified the same predominance of human and gull markers in stormwater and beach locations, respectively; however, the dPCR multiplex assay was more sensitive and capable of detecting fecal contamination that was undetected by qPCR assays. These results demonstrate the dPCR assay used in this study could be a viable tool for MST studies to increase the ability to identify low levels of fecal contamination.IMPORTANCE Fecal contamination of recreational water poses a persistent and ongoing problem, particularly in areas of concern around the Great Lakes. The identification of the source(s) of fecal contamination is essential for safeguarding public health as well as guiding remediation efforts; however, fecal contamination may frequently be present at low levels and remain undetectable by certain methodologies. In this study, we utilized microbial source tracking techniques using both quantitative and digital PCR assays to identify sources of contamination. Our results indicated high levels of human fecal contamination within stormwater outfalls, while lower levels were observed throughout the watershed. Additionally, high levels of gull fecal contamination were detected at Rouge Beach, particularly during drier sampling events. Furthermore, our results indicated an increased sensitivity of the digital PCR assay to detect both human and gull contamination, suggesting it could be a viable tool for future microbial source tracking studies.