Linking fecal bacteria in rivers to landscape, geochemical, and hydrologic factors and sources at the basin scale

Evaluation of Grower-Friendly, Science-Based Sampling Approaches for the Detection of Salmonella in Ponds Used for Irrigation of Fresh Produce

The recognition that irrigation water sources contribute to preharvest contamination of produce has led to new regulations on testing microbial water quality. To best identify contamination problems, growers who depend on irrigation ponds need guidance on how and where to collect water samples for testing. In this study, we evaluated several sampling strategies to identify Salmonella and Escherichia coli contamination in five ponds used for irrigation on produce farms in southern Georgia. Both Salmonella and E. coli were detected regularly in all the ponds over the 19-month study period, with overall prevalence and concentrations increasing in late summer and early fall. Of 507 water samples, 217 (42.8%) were positive for Salmonella, with a very low geometric mean (GM) concentration of 0.06 most probable number (MPN)/100 mL, and 442 (87.1%) tested positive for E. coli, with a GM of 6.40 MPN/100 mL. We found no significant differences in Salmonella or E. coli detection rates or concentrations between sampling at the bank closest to the pump intake versus sampling from the bank around the pond perimeter, when comparing with results from the pump intake, which we considered our gold standard. However, samples collected from the bank closest to the intake had a greater level of agreement with the intake (Cohen's kappa statistic = 0.53; p < 0.001) than the samples collected around the pond perimeter (kappa = 0.34; p = 0.009). E. coli concentrations were associated with increased odds of Salmonella detection (odds ratio = 1.31; 95% confidence interval = 1.10-1.56). All the ponds would have met the Produce Safety Rule standards for E. coli, although Salmonella was also detected. Results from this study provide important information to growers and regulators about pathogen detection in irrigation ponds and inform best practices for surface water sampling.

Regional Variations of Bovine and Porcine Fecal Pollution as a Function of Landscape, Nutrient, and Hydrological Factors

The effects of manure application in agriculture on surface water quality has become a local to global problem because of the adverse consequences on public health and food security. This study evaluated (i) the spatial distribution of bovine (cow) and porcine (pig) genetic fecal markers, (ii) how hydrologic factors influenced these genetic markers, and (iii) their variations as a function of land use, nutrients, and other physiochemical factors. We collected 189 samples from 63 watersheds in Michigan's Lower Peninsula during baseflow, spring melt, and summer rain conditions. For each sample, we quantified the concentrations of bovine and porcine genetic markers by digital droplet polymerase chain reaction and measured , dissolved oxygen, pH, temperature, total phosphorus, total nitrogen, nitrate-nitrite (NO), ammonia (NH), soluble reactive phosphorus, streamflow, and watershed specific precipitation. Bovine and porcine manure markers were ubiquitous in rivers that drain agricultural and natural fields across the study region. This study provides baseline conditions on the state of watershed impairment, which can be used to develop best management practices that could improve water quality. Similar studies should be performed with higher spatial sampling density to elucidate detailed factors that influence the transport of manure constituents.

Clostridium perfringens identifies source of pollution and reference streams in a tropical highland environment

Clostridium perfringens was analysed in soils from a tropical highland catchment and corresponding headwater streams at baseflow condition in order to understand the contribution of soils to the microbiological quality of stream water and the feasibility of using these streams as surrogate for negative control (reference streams). The concentrations of C. perfringens depended on the sample matrix. C. perfringens concentrations were significantly higher in the catchment soil than in the stream water (P < 0.05, n = 20). In addition, C. perfringens concentrations in the catchment soil remarkably predicted C. perfringens concentrations in the stream water (i.e., 82% of variations in C. perfringens concentrations in water were predicted by C. perfringens concentrations in soil; P < 0.05, n = 20). This suggests that the catchment soils contributed C. perfringens to the stream water. Despite the observed contamination, the concentrations of C. perfringens (geometric mean of 32 cfu/100 cm³) in the stream water was below the recommended safe level for tropical freshwater systems and extremely lower than that detected in anthropogenically influenced rivers. This concentration was defined as an acceptable level of disturbance, and a reference concentration that can serve as surrogate for negative control in the studied tropical environment.

Assessment of the decay rates of microbial source tracking molecular markers and faecal indicator bacteria from different sources

AIMS

Evaluate the T90 and compare the decay of different faecal indicator bacteria (FIB) and molecular microbial source tracking (MST) markers of human and animal sources during summer and winter.

METHODS AND RESULTS

The persistence of Escherichia coli and enterococci and several MST molecular markers targeting host-specific Bifidobacterium and Bacteroidales species (BifHM, BifCW, BifPL, HF183/BFD, Rum2Bac and Pig2Bac) was assessed at the same time using mesocosms. Dialysis bags filled with diluted wastewater from different sources were kept in an outdoor water tank and monitored regularly to assess the inactivation rates. The T90 values of E. coli by culture methods ranged from 1·52 to 5·69 days in summer and 2·06 to 6·19 days in winter, whereas with qPCR 2·29-4·23 days in summer and 4·17-8·09 days in winter. T90 values for enterocci ranged from 1·15 to 3·10 days in summer and from 3·01 to 5·46 days in winter. Significant differences were observed between faecal sources for both markers. For the MST makers similar T90 values were obtained in summer (1·05-1·91 days), whereas higher variability was observed in winter (2·90-6·12 days).

CONCLUSIONS

Different decay rates were observed for the FIB from the different sources, especially for E. coli in ruminant samples. A higher variability among T90 values of the different MST markers in winter was observed, whereas similar T90 values were detected in summer highlighting the stronger effect of environmental parameters during this season.

SIGNIFICANCE AND IMPACT OF THE STUDY

The diverse inactivation rates observed in bacteria from different faecal sources have implications when these rates are used to model faecal pollution in water. The use of FIBT90 of different sources is essential to develop reliable predictive models. Since different inactivation of E. coli regarding the source of pollution has been observed, the source of the pollution has to be considered for modelling approaches.

Correlation of crAssphage qPCR Markers with Culturable and Molecular Indicators of Human Fecal Pollution in an Impacted Urban Watershed

Environmental waters are monitored for fecal pollution to protect public health. Many previously developed human-specific fecal pollution indicators lack adequate sensitivity to be reliably detected in environmental waters or do not correlate well with viral pathogens. Recently, two novel human sewage-associated source tracking qPCR markers were developed based on the bacteriophage crAssphage, CPQ_056 and CPQ_064. These assays are highly human specific, abundant in sewage, and are viral-based, suggesting great promise for environmental application as human fecal pollution indicators. A 30-day sampling study was conducted in an urban stream impacted by combined sewer overflows to evaluate the crAssphage markers' performance in an environmental system. The crAssphage markers were present at concentrations of 4.02-6.04 log₁₀ copies/100 mL throughout the study period, indicating their high abundance and ease of detection in polluted environmental waters. In addition, the crAssphage assays were correlated with rain events, molecular markers for human polyomavirus and HF183, as well as culturable E. coli, enterococci, and somatic coliphage. The CPQ_064 assay correlated strongly to a greater number of biological indicators than the CPQ_056 assay. This study is the first to evaluate both crAssphage qPCR assays in an extended environmental application of crAssphage markers for monitoring of environmental waters. It is also the first study to compare crAssphage marker concentration with other viral-based indicators.

High levels of sewage contamination released from urban areas after storm events: A quantitative survey with sewage specific bacterial indicators

BACKGROUND

Past studies have demonstrated an association between waterborne disease and heavy precipitation, and climate change is predicted to increase the frequency of these types of intense storm events in some parts of the United States. In this study, we examined the linkage between rainfall and sewage contamination of urban waterways and quantified the amount of sewage released from a major urban area under different hydrologic conditions to identify conditions that increase human risk of exposure to sewage.

METHODS AND FINDINGS

Rain events and low-flow periods were intensively sampled to quantify loads of sewage based on two genetic markers for human-associated indicator bacteria (human Bacteroides and Lachnospiraceae). Samples were collected at a Lake Michigan estuary and at three river locations immediately upstream. Concentrations of indicators were analyzed using quantitative polymerase chain reaction (qPCR), and loads were calculated from streamflow data collected at each location. Human-associated indicators were found during periods of low flow, and loads increased one to two orders of magnitude during rain events from stormwater discharges contaminated with sewage. Combined sewer overflow (CSO) events increased concentrations and loads of human-associated indicators an order of magnitude greater than heavy rainfall events without CSO influence. Human-associated indicator yields (load per km2 of land per day) were related to the degree of urbanization in each watershed. Contamination in surface waters were at levels above the acceptable risk for recreational use. Further, evidence of sewage exfiltration from pipes threatens drinking water distribution systems and source water. While this study clearly demonstrates widespread sewage contamination released from urban areas, a limitation of this study is understanding human exposure and illness rates, which are dependent on multiple factors, and gaps in our knowledge of the ultimate health outcomes.

CONCLUSIONS

With the prediction of more intense rain events in certain regions due to climate change, sewer overflows and contamination from failing sewer infrastructure may increase, resulting in increases in waterborne pathogen burdens in waterways. These findings quantify hazards in exposure pathways from rain events and illustrate the additional stress that climate change may have on urban water systems. This information could be used to prioritize efforts to invest in failing sewer infrastructure and create appropriate goals to address the health concerns posed by sewage contamination from urban areas.

Host-Specific Bacteroides Markers-Based Microbial Source Tracking in Aquaculture Areas

Various waterborne pathogens originate from human or animal feces and may cause severe gastroenteric outbreaks. Bacteroides spp. that exhibit strong host- or group-specificities are promising markers for identifying fecal sources and their origins. In the present study, 240 water samples were collected from two major aquaculture areas in Republic of Korea over a period of approximately 1 year, and the concentrations and occurrences of four host-specific Bacteroides markers (human, poultry, pig, and ruminant) were evaluated in the study areas. Host-specific Bacteroides markers were detected widely in the study areas, among which the poultry-specific Bacteroides marker was detected at the highest concentration (1.0-1.2 log₁₀ copies L^-1). During the sampling period, high concentrations of host-specific Bacteroides markers were detected between September and December 2015. The host-specific Bacteroides marker-combined geospatial map revealed the up-to-downstream gradient of fecal contamination, as well as the effects of land-use patterns on host-specific Bacteroides marker concentrations. In contrast to traditional bacterial indicators, the human-specific Bacteroides marker correlated with human specific pathogens, such as noroviruses (r=0.337; P<0.001). The present results indicate that host-specific Bacteroides genetic markers with an advanced geospatial analysis are useful for tracking fecal sources and associated pathogens in aquaculture areas.

Human dissemination of genes and microorganisms in Earth's Critical Zone

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.

Sewage loading and microbial risk in urban waters of the Great Lakes

Despite modern sewer system infrastructure, the release of sewage from deteriorating pipes and sewer overflows is a major water pollution problem in US cities, particularly in coastal watersheds that are highly developed with large human populations. We quantified fecal pollution sources and loads entering Lake Michigan from a large watershed of mixed land use using host-associated indicators. Wastewater treatment plant influent had stable concentrations of human Bacteroides and human Lachnospiraceae with geometric mean concentrations of 2.77 × 10⁷ and 5.94 × 10⁷ copy number (by quantitative PCR) per 100 ml, respectively. Human-associated indicator levels were four orders of magnitude higher than norovirus concentrations, suggesting that these human-associated bacteria could be sensitive indicators of pathogen risk. Norovirus concentrations in these same samples were used in calculations for quantitative microbial risk assessment. Assuming a typical recreational exposure to untreated sewage in water, concentrations of 7,800 copy number of human Bacteroides per 100 mL or 14,000 copy number of human Lachnospiraceae per 100 mL corresponded to an illness risk of 0.03. These levels were exceeded in estuarine waters during storm events with greater than 5 cm of rainfall. Following overflows from combined sewer systems (which must accommodate both sewage and stormwater), concentrations were 10-fold higher than under rainfall conditions. Automated high frequency sampling allowed for loads of human-associated markers to be determined, which could then be related back to equivalent volumes of untreated sewage that were released. Evidence of sewage contamination decreased as ruminant-associated indicators increased approximately one day post-storm, demonstrating the delayed impact of upstream agricultural sources on the estuary. These results demonstrate that urban areas are a diffuse source of sewage contamination to urban waters and that storm-driven release of sewage, particularly when sewage overflows occur, creates a serious though transient human health risk.

Septic systems contribute to nutrient pollution and harmful algal blooms in the St. Lucie Estuary, Southeast Florida, USA

Nutrient enrichment is a significant global-scale driver of change in coastal waters, contributing to an array of problems in coastal ecosystems. The St. Lucie Estuary (SLE) in southeast Florida has received national attention as a result of its poor water quality (elevated nutrient concentrations and fecal bacteria counts), recurring toxic Microcystis aeruginosa blooms, and its proximity to the northern boundary of tropical coral species in the United States. The SLE has an artificially large watershed comprised of a network of drainage canals, one of which (C-44) is used to lower the water level in Lake Okeechobee. Public attention has primarily been directed at nutrient inputs originating from the lake, but recent concern over the importance of local watershed impacts prompted a one-year watershed study designed to investigate the interactions between on-site sewage treatment and disposal systems (OSTDS or septic systems), groundwaters, and surface waters in the SLE and nearshore reefs. Results provided multiple lines of evidence of OSTDS contamination of the SLE and its watershed: 1) dissolved nutrients in groundwaters and surface waters were most concentrated adjacent to two older (pre-1978) residential communities and the primary canals, and 2) sucralose was present in groundwater at residential sites (up to 32.0μg/L) and adjacent surface waters (up to 5.5μg/L), and 3) δ¹⁵N values in surface water (+7.5 ^o/_oo), macroalgae (+4.4 ^o/_oo) and phytoplankton (+5.0 ^o/_oo) were within the published range (>+3 ^o/_oo) for sewage N and similar to values in OSTDS-contaminated groundwaters. Measured δ¹⁵N values in M. aeruginosa became increasingly enriched during transport from the C-44 canal (∼5.8 ^o/_oo) into the mid-estuary (∼8.0 ^o/_oo), indicating uptake and growth on sewage N sources within the urbanized estuary. Consequently, there is a need to reduce N and P loading, as well as fecal loading, from the SLE watershed via septic-to-sewer conversion projects and to minimize the frequency and intensity of the releases from Lake Okeechobee to the SLE via additional water storage north of the lake. These enhancements would improve water quality in both the SLE and Lake Okeechobee, reduce the occurrence of toxic harmful algal blooms in the linked systems, and improve overall ecosystem health in the SLE and downstream reefs.

Microbial communities as biosensors for monitoring urban environments

The BE microbiome is a naturally embedded biosensor in urban infrastructure that can be used to monitor environmental quality and human activity. There are many potential opportunities for leveraging BE microbial communities to guide urban design and public health policy.

Significance of beach geomorphology on fecal indicator bacteria levels

Large databases of fecal indicator bacteria (FIB) measurements are available for coastal waters. With the assistance of satellite imagery, we illustrated the power of assessing data for many sites by evaluating beach features such as geomorphology, distance from rivers and canals, presence of piers and causeways, and degree of urbanization coupled with the enterococci FIB database for the state of Florida. We found that beach geomorphology was the primary characteristic associated with enterococci levels that exceeded regulatory guidelines. Beaches in close proximity to marshes or within bays had higher enterococci exceedances in comparison to open coast beaches. For open coast beaches, greater enterococci exceedances were associated with nearby rivers and higher levels of urbanization. Piers and causeways had a minimal contribution, as their effect was often overwhelmed by beach geomorphology. Results can be used to understand the potential causes of elevated enterococci levels and to promote public health.

A case study characterizing animal fecal sources in surface water using a mitochondrial DNA marker

Water quality impairment by fecal waste in coastal watersheds is a public health issue. The present study provided evidence for the use of a mitochondrial (mtDNA) marker to detect animal fecal sources in surface water. The accurate identification of fecal pollution is based on the notion that fecal microorganisms preferentially inhabit a host animal's gut environment. In contrast, mtDNA host-specific markers are inherent to eukaryotic host cells, which offers the advantage by detecting DNA from the host rather than its fecal bacteria. The present study focused on sampling water presumably from non-point sources (NPS), which can increase bacterial and nitrogen concentrations to receiving water bodies. Stream sampling sites located within the Piscataqua River Watershed (PRW), New Hampshire, USA, were sampled from a range of sites that experienced nitrogen inputs such as sewer and septic systems and suburban runoff. Three mitochondrial (mtDNA) gene marker assays (human, bovine, and canine) were tested from surface water. Nineteen sites were sampled during an 18-month period. Analyses of the combined single and multiplex assay results showed that the proportion of occurrence was highest for bovine (15.6%; n = 77) compared to canine (5.6%; n = 70) and human (5.7%; n = 107) mtDNA gene markers. For the human mtDNA marker, there was a statistically significant relationship between presence vs. absence and land use (Fisher's test p = 0.0031). This result was evident particularly for rural suburban septic, which showed the highest proportion of presence (19.2%) compared to the urban sewered (3.3%), suburban sewered (0%), and agricultural (0%) as well as forested septic (0%) sites. Although further testing across varied land use is needed, our study provides evidence for using the mtDNA marker in large watersheds.

Bacteroidales markers for microbial source tracking in Southeast Asia

The island city country of Singapore served as a model to validate the use of host-associated Bacteroidales 16S rRNA gene marker assays for identifying sources of fecal pollution in the urban tropical environment of Southeast Asia. A total of 295 samples were collected from sewage, humans, domesticated animals (cats, dogs, rabbits and chicken), and wild animals (birds, monkeys and wild boars). Samples were analyzed by real time PCR using five human-associated assays (HF183-SYBR Green, HF183, BacHum, BacH and B. thetaiotaomicron α-1-6, mannanase (B. theta), one canine-associated assay (BacCan), and a total Bacteroidales assay (BacUni). The best performing human-associated assay was B. theta with a diagnostic sensitivity of 69% and 100% in human stool and sewage, respectively, and a specificity of 98%. BacHum achieved the second highest sensitivity and specificity for human stool at 65% and 91%, respectively. The canine-associated Bacteroidales assay (BacCan) had a sensitivity and specificity above 80% and was validated for tracking fecal pollution from dogs. BacUni demonstrated a sensitivity and specificity of 100% for mammals, thus BacUni was confirmed for total Bacteroidales detection in the region. We showed for the first time that rabbit fecal samples cross-react with human-associated assays (HF183-SYBR Green, HF183, BacHum and BacH) and with BacCan. Our findings regarding the best performing human-associated assays differ from those reported in Bangladesh and India, which are geographically close to Southeast Asia, and where HF183 and BacHum were the preferred assays, respectively.

Community-Level Sanitation Coverage More Strongly Associated with Child Growth and Household Drinking Water Quality than Access to a Private Toilet in Rural Mali

Sanitation access can provide positive externalities; for example, safe disposal of feces by one household prevents disease transmission to households nearby. However, little empirical evidence exists to characterize the potential health benefits from sanitation externalities. This study investigated the effect of community sanitation coverage versus individual household sanitation access on child health and drinking water quality. Using a census of 121 villages in rural Mali, we analyzed the association of community latrine coverage (defined by a 200 m radius surrounding a household) and individual household latrine ownership with child growth and household stored water quality. Child height-for-age had a significant and positive linear relationship with community latrine coverage, while child weight-for-age and household water quality had nonlinear relationships that leveled off above 60% coverage (p < 0.01; generalized additive models). Child growth and water quality were not associated with individual household latrine ownership. The relationship between community latrine coverage and child height was strongest among households without a latrine; for these households, each 10% increase in latrine coverage was associated with a 0.031 (p-value = 0.040) increase in height-for-age z-score. In this study, the level of sanitation access of surrounding households was more important than private latrine access for protecting water quality and child health.

Isolating the impact of septic systems on fecal pollution in streams of suburban watersheds in Georgia, United States

The presence of multiple sources of fecal pollution at the watershed level presents challenges to efforts aimed at identifying the influence of septic systems. In this study multiple approaches including targeted sampling and monitoring of host-specific Bacteroidales markers were used to identify the impact of septic systems on microbial water quality. Twenty four watersheds with septic density ranging from 8 to 373 septic units/km² were monitored for water quality under baseflow conditions over a 3-year period. The levels of the human-associated HF183 marker, as well as total and ruminant Bacteroidales, were quantified using quantitative polymerase chain reaction. Human-associated Bacteroidales yield was significantly higher in high density watersheds compared to low density areas and was negatively correlated (r = -0.64) with the average distance of septic systems to streams in the spring season. The human marker was also positively correlated with the total Bacteroidales marker, suggesting that the human source input was a significant contributor to total fecal pollution in the study area. Multivariable regression analysis indicates that septic systems, along with forest cover, impervious area and specific conductance could explain up to 74% of the variation in human fecal pollution in the spring season. The results suggest septic system impact through contributions to groundwater recharge during baseflow or failing septic system input, especially in areas with >87 septic units/km². This study supports the use of microbial source tracking approaches along with traditional fecal indicator bacteria monitoring and land use characterization in a tiered approach to isolate the influence of septic systems on water quality in mixed-use watersheds.

Association of land use and its change with beach closure in the United States, 2004-2013

Land use and its change have great influences on water quality. However, their impacts on microbial contamination of beach water have rarely been investigated and their relationship with beach actions (e.g., advisories or closure) is still unknown. Here, we analyzed beach closure data obtained from 2004 to 2013 for >500 beaches in the United States, and examined their associations with land use around beaches in 2006 and 2011, as well as the land use change between 2006 and 2011. The results show that the number of beach closures due to elevated indicators of health risk is negatively associated with the percentages of forest, barren land, grassland and wetland, while positively associated with the percentages of urban area. The results from multi-level models also indicate the negative association with forest area but positive association with urban area and agriculture. The examination of the change of land use and the number of beach closures between 2006 and 2011 indicates that the increase in the number of beach closures is positively associated with the increase in urban (β=1.612, p<0.05) and agricultural area including pasture (β=0.098, p<0.05), but negatively associated with the increase in forest area (β=-1.789, p<0.05). The study suggests that urbanization and agriculture development near beaches have adverse effects on beach microbial water quality, while afforestation may protect beach water quality and reduce the number of beach closures.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls

Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log₁₀ copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log₁₀ CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log₁₀ CFU/100 ml, and 7.65 log₁₀ CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds.

IMPORTANCE

Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls

Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log₁₀ copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log₁₀ CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log₁₀ CFU/100 ml, and 7.65 log₁₀ CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds.

IMPORTANCE

Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination.

Comparative microbial source tracking methods for identification of fecal contamination sources at Sunnyside Beach in the Toronto region area of concern

Several beaches within the Toronto region area of concern have persistent issues with fecal contamination, causing a beach beneficial use impairment (BUI). In this study, Escherichia coli, including ampicillin-resistant strains, were enumerated via culturable and quantitative polymerase chain reaction (qPCR) methods. Microbial source tracking (MST) markers (for general Bacteroidales, human, ruminant/cow, gull, and dog) were detected and enumerated via PCR and qPCR to identify sources of fecal contamination at Sunnyside Beach and in the Humber River. Human, cow, and dog markers had good host-specificity, while gull markers sometimes amplified a few other bird species. The ruminant endpoint PCR marker amplified a variety of other animal species rendering it less useful. Both human and gull fecal contamination were prevalent in the Humber River, while Sunnyside Beach was predominantly impacted by gull fecal contamination. Human sewage impacts were more prevalent in the lower Humber River, particularly in Black Creek. However, to reduce Sunnyside beach postings, reducing bird fecal contamination in the river and at the beach would be necessary. When there are high levels of E. coli throughout a beachshed, an MST toolbox approach can add value to discriminate source(s) of E. coli contamination and guide decisions relating to public health risk and remediation strategies.

The microbiome of urban waters

More than 50% of the world's population lives in urban centers. As collection basins for landscape activity, urban waters are an interface between human activity and the natural environment. The microbiome of urban waters could provide insight into the impacts of pollution, the presence of human health risks, or the potential for long-term consequences for these ecosystems and the people who depend upon them. An integral part of the urban water cycle is sewer infrastructure. Thousands of miles of pipes line cities as part of wastewater and stormwater systems. As stormwater and sewage are released into natural waterways, traces of human and animal microbiomes reflect the sources and magnitude of fecal pollution and indicate the presence of pollutants, such as nutrients, pathogens, and chemicals. Non-fecal organisms are also released as part of these systems. Runoff from impervious surfaces delivers microbes from soils, plants and the built environment to stormwater systems. Further, urban sewer infrastructure contains its own unique microbial community seemingly adapted to this relatively new artificial habitat. High microbial densities are conveyed via pipes to waterways, and these organisms can be found as an urban microbial signature imprinted on the natural community of rivers and urban coastal waters. The potential consequences of mass releases of non-indigenous microorganisms into natural waters include creation of reservoirs for emerging human pathogens, altered nutrient flows into aquatic food webs, and increased genetic exchange between two distinct gene pools. This review highlights the recent characterization of the microbiome of urban sewer and stormwater infrastructure and its connection to and potential impact upon freshwater systems.