Microbial source tracking of fecal pollution to coral reef lagoons of Norfolk Island, Australia

Fecal pollution contributes to global degradation of water quality and requires identification of the source(s) for predicting human health risk, tracking disease, and developing management strategies. While fecal indicator bacteria are commonly used to detect fecal pollution, they cannot identify sources. Novel approaches, such as microbial source tracking (MST), can be applied to evaluate the origin of fecal pollution. This study examined fecal pollution in the coral reef lagoons of Norfolk Island, Australia where reef health decline has been related to nutrient input. The primary objective of this study was to evaluate the host sensitivity and specificity of two human wastewater-associated marker genes (Bacteroides HF183 (HF183) and cross-assembly phage (crAssphage)) and four animal feces associated marker genes targeting avian, ruminant, dog, and pig (Helicobacter-associated GFD (GFD), Bacteroides BacR (BacR), Bacteroides DogBact (DogBact), and Bacteroides Pig-2-Bac (Pig-2-Bac)) in wastewater and animal fecal samples collected from Norfolk Island. The prevalence and concentrations of these marker genes along with enterococci genetic marker (ENT 23S rRNA) of general fecal pollution and human adenovirus (HAdV), which is considered predominantly a pathogen but also a human-wastewater associated marker gene, were determined in surface, ground, and marine water resources. A secondary objective of this study was to assess the sources and pathways of fecal pollution to a sensitive marine environment under rainfall events. HF183, crAssphage, HAdV, and BacR demonstrated absolute host sensitivity values of 1.00, while GFD and Pig-2-Bac had host sensitivity values of 0.60, and 0.20, respectively. Host specificity values were > 0.94 for all marker genes. Human and animal (avian, ruminant, dog) fecal sources were present in the coral reef lagoons and surface water whereas groundwater was polluted by human wastewater markers. This study provides understanding of fecal pollution in water resources on Norfolk Island, Australia after precipitation events. The results may aid in effective water quality management, mitigating potential adverse effects on both human and environmental health.

The host specificity of pilus gene traA in Escherichia coli and its use in tracking human fecal pollution

A reliable and accurate fecal source tracking (FST) approach is important in water quality management and preventing foodborne and waterborne diseases. In this study, a genetic marker of Escherichia coli (E. coli) was identified and utilized to differentiate between human and animal sources of fecal contamination. Nucleotide polymorphisms of 14 genes coding for cellular surface proteins, mainly fimbriae, were analyzed using the 22 draft genomes of E. coli strains from human and three domestic animal sources in Japan. A signature sequence, traAh, within the pilin gene traA, was found to be highly associated with E. coli of human origin. Subsequently, an end-point polymerase chain reaction (PCR) assay, namely PCR-Htra, was developed, specifically targeting traAh. The high association between traAh and E. coli of human origin was validated through the PCR-Htra amplification. This encompassed 1045 E. coli strains isolated from surface water, human feces or sewages, and feces from 12 animal species, including domestic and wild animals in the states of Missouri and Virginia in the United States of America (USA). The data suggested that the sensitivity and specificity of PCR-Htra assay were 49.0 % and 99.5 % respectively in distinguishing human-origin E. coli from nonhuman-source ones. Furthermore, the result of our in silico analysis of GenBank® data suggests that traAh may have a global distribution as the sequence was found in human-origin E. coli isolated from at least 14 countries around the world. Thus, the PCR-Htra may provide a new FST tool for rapid and accurate detection of human-origin E. coli, serving as a means to identify human fecal contamination in water.

Detection and Quantification of Bacteriophages in Wastewater Samples by Culture and Molecular Methods

Bacteriophages are promising tools for the detection of fecal pollution in water bodies and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages are perfect surrogates for the study of the fate and transport of enteric viruses, generally better than any other group of indicators.Different groups of bacteriophages, such as somatic coliphages, F-specific RNA bacteriophages, and bacteriophages infecting selected strains of Bacteroides, have been comprehensively tested as indicators of fecal pollution. Somatic coliphages and F-specific RNA bacteriophages can be used as indicators of general fecal contamination, whereas Bacteroides phages can be used to detect a particular fecal source, for instance, human, bovine, porcine, or poultry fecal contamination.Feasible and cost-effective protocols standardized by the International Standardization Organization and the United States Environmental Protection Agency for the detection of infectious bacteriophages belonging to these three groups are available. Molecular methods for the detection of some particular phages have also been developed. Here we introduce those methods for the detection, enumeration, and isolation of bacteriophages in wastewater samples.

Tracking the sources of Leptospira and nutrient flows in two urban watersheds of Puerto Rico

This study investigated the relationship between nutrient levels, source of fecal contamination, and pathogenic Leptospira in Puerto Rico's northern coast and San Juan Bay Estuary (SJBE) aquatic ecosystems. Microbial source tracking (MST) was also used to investigate the connections between sources of feces contamination and the presence of Leptospira. Eighty-seven water samples were collected during the June (n=44) and August (n=43) in 2020. To quantify phosphorus and nitrogen concentrations, standard USEPA protocols were utilized, specifically Methods 365.4 for total and dissolved phosphorus, 351.2 for total Kjeldahl nitrogen and ammonium, and 353.2 for nitrate. Lipl32 gene-specific quantitative polymerase chain reaction (qPCR) was used to detect the presence of Leptospira. Human (HF183), canine (BacCan-UCD), and equine (HoF597) MST assays were utilized to trace the origins of fecal contamination. Forty one percent of the locations exceeded Puerto Rico's authorized total phosphorus limit of 160 g L-1, while 34% exceeded the total nitrogen limit of 1700 g L-1. Nearly half of the streams examined are affected by eutrophication. The MST analysis identified human and canine feces as the most prevalent contaminants, affecting approximately 50% of the sites. In addition, Leptospira was detected in 32% of the June samples. There was a significant correlation (r = 0.79) between the incidence of pathogenic Leptospira and the human bacterial marker (HF183). This study illuminates the central role of anthropogenic inputs in nutrient enrichment and pathogen proliferation in Puerto Rico's aquatic ecosystems.

Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study

With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.

Low antimicrobial resistance in Escherichia coli isolates from two large Austrian alpine karstic spring catchments

The increased occurrence of antibiotic resistant bacteria poses a threat to global public health. Clinically relevant resistances also spread through the environment. Aquatic ecosystems in particular represent important dispersal pathways. In the past, pristine water resources have not been a study focus, although ingestion of resistant bacteria through water consumption constitutes a potentially important transmission route. This study assessed the antibiotic resistances in Escherichia coli populations in two large well-protected and well-managed Austrian karstic spring catchments representing essential groundwater resources for water supply. E. coli were detected seasonally only during the summer period. By screening a representative number of 551 E. coli isolates from 13 sites in two catchments, it could be shown that the prevalence of antibiotic resistance in this study area is low. 3.4 % of the isolates showed resistances to one or two antibiotic classes, 0.5 % were resistant to three antibiotic classes. No resistances to critical and last-line antibiotics were detected. By integrating fecal pollution assessment and microbial source tracking, we could infer that ruminants were the main hosts for antibiotic resistant bacteria in the studied catchment areas. A comparison with other studies on antibiotic resistances in karstic or mountainous springs highlighted the low contamination status of the model catchments studied here, most likely due to the high protection and careful management while other, less pristine catchments showed much higher antibiotic resistances. We demonstrate that studying easily accessible karstic springs allows a holistic view on large catchments concerning the extent and origin of fecal pollution as well as antibiotic resistance. This representative monitoring approach is also in line with the proposed update of the EU Groundwater Directive (GWD).

Using watershed characteristics to enhance fecal source identification

Fecal pollution is one of the most prevalent forms of pollution affecting waterbodies worldwide, threatening public health and negatively impacting aquatic environments. Microbial source tracking (MST) applies polymerase chain reaction (PCR) technology to help identify the source of fecal pollution. In this study, we combine spatial data for two watersheds with general and host-associated MST markers to target human (HF183/BacR287), bovine (CowM2), and general ruminant (Rum2Bac) sources. Concentrations of MST markers in samples were determined with droplet digital PCR (ddPCR). The three MST markers were detected at all sites (n = 25), but bovine and general ruminant markers were significantly associated with watershed characteristics. MST results, combined with watershed characteristics, suggest that streams draining areas with low-infiltration soil groups and high agricultural land use are at an increased risk for fecal contamination. Microbial source tracking has been applied in numerous studies to aid in identifying the sources of fecal contamination, but these studies usually lack information on the involvement of watershed characteristics. Our study combined watershed characteristics with MST results to provide more comprehensive insight into the factors that influence fecal contamination in order to implement the most effective best management practices.

Spatial distribution of fecal pollution indicators in sewage sludge flocs and their removal and inactivation as revealed by qPCR/viability-qPCR during potassium ferrate treatment

Sludge reuse and utilization is one of important routines of disseminating fecal pollution to surface water and groundwater. However, it remains unclear the spatial distribution of fecal pollution indicators in sludge flocs and their reductions during sludge treatment processes. In this study, the abundances of fecal pollution indicators including cross-assembly phage (crAssphage), JC and BK polyomavirus (JCPyV, BKPyV), human adenovirus (HAdV), the human-specific HF183 Bacteroides (HF183) and Escherichia coli (EC) in soluble extracellular polymeric substances (S-EPS), loosely-bound EPS (LB-EPS), tightly-bound EPS (TB-EPS), and pellets of sludge flocs were determined, and the effect of potassium ferrate (PF) treatment on their removal and inactivation was investigated by using both qPCR and viability-qPCR. Results showed that all investigated indicators were detected in each fraction of sludge flocs. The PF treatment led to a great migration of indicators from sludge pellets to sludge EPS and some extent of their inactivation in each fraction of sludge flocs. The overall reductions of human fecal indicators in sludge determined by qPCR were 0-1.30 logs, which were 0-2 orders of magnitude lower than those of 0.69-2.39 logs detected by viability-qPCR, implying their inactivation by PF treatment to potentially alleviate the associated human health risks.

Predictive modeling of microbiological seawater quality in karst region using cascade model

This paper presents an in-depth analysis of seawater quality measurements during the bathing seasons from year 2009 to 2020 in the city of Rijeka, Croatia. Due to rare occurrences of measurements with less than excellent water quality, considered dataset is deeply imbalanced. Additionally, it incorporates measurements under the influence of submerged groundwater discharges (SGD), which were observed in some bathing locations. These discharges were previously thought to dry up during the summer season and are now suspected to be one of the causes of increased Escherichia coli values. Consequently, and in view of the fact that the accuracy of prediction models can be significantly influenced by temporal and spatial variation of the input data, a novel cascade prediction modeling strategy was proposed. It consists of a sequence of prediction models which tend to identify general environmental conditions which confidently lead to excellent bathing water quality. The proposed model uses environmental features which can rather easily be estimated or obtained from the weather forecast. The model was trained on a highly biased dataset, consisting of data from locations with and without SGD influence, and for the time period spanning extremely dry and warm seasons, extremely wet seasons, as well as normal seasons. To simulate realistic application, the model was tested using temporal and spatial stratification of data. The cascade strategy was shown to be a good approach for reliably detecting environmental parameters which produce excellent water quality. Proposed model is designed as a filter method, where instances classified as less-than-excellent water quality require further analysis. The cascade model provides great flexibility as it can be customized to the particular needs of the investigated area and dataset specifics.

Escherichia cryptic clade II through clade VIII: Rapid detection and prevalence in feces and surface water

Bacteria of the cryptic lineage of genus Escherichia, or Escherichia cryptic clades (cryptic clades), are phenotypically indistinguishable from Escherichia coli (E. coli) using standard biochemical tests. Except for clade I (C-I), cryptic clades were hypothetically believed to be environmental but not enteric. If so, they would hinder the interpretation of current E. coli-based water quality (fecal pollution) monitoring in the United States because environmental bacteria do not indicate the presence of harmful fecal material. This study was performed to develop a rapid method for the detection of cryptic clades and to investigate their potential impact on water quality monitoring. By whole-genome comparison, one gene, named ecc (Escherichiacryptic clades), was identified to be unique to C-II through C-VIII. An end-point polymerase chain reaction (PCR) method, eccPCR, was developed by targeting the ecc. The results of in-silico and wet tests demonstrated 100 % sensitivity and specificity of the eccPCR to detect C-II through C-VIII. Based on the EPA Method 1603, 519 presumptive E. coli isolates were obtained from the fecal samples of 13 different host species and 192 isolates from surface water samples taken at four locations in a watershed of mid-Missouri. As indicated by the eccPCR amplification, the overall prevalence of C-II through C-VIII in the presumptive E. coli isolates was estimated to be about 0.6 % in the fecal samples and about 1.6 % in the water samples. Therefore, the potential impact of cryptic clades on water quality monitoring may be limited if EPA Method 1603 is used. Furthermore, clades C-II through C-VIII in stream water samples were found repeatedly only at a single sampling site, but neither at the upstream sites nor five kilometers downstream of the site. The data do not support nor reject the environmental hypothesis about cryptic clades. Further study is needed to determine the implication of the observation.

Distribution and correlation between antibiotic resistance genes and host-associated markers before and after swine fever in the longjiang watershed

Antibiotic resistance genes (ARGs) are abundantly shed in feces. Thus, it is crucial to identify their host sources so that ARG pollution can be effectively mitigated and aquatic ecosystems can be properly conserved. Here, spatiotemporal variations and sources of ARGs in the Longjiang watershed of South China were investigated by linking them with microbial source tracker (MST) indicators. The most frequently detected ARGs (>90%) were sulI, sulII, bla_TEM, tetW, ermF, and the mobile element intI1. Spatial distribution analyses showed that tributaries contributed significantly more sulI, sulII, and ermF contamination to the Longjiang watershed than the main channel. MST indicator analysis revealed that the Longjiang watershed was contaminated mainly by human fecal pollution. Livestock- and poultry-associated fecal pollution significantly declined after the swine fever outbreak. The occurrence of most ARGs is largely explained by human fecal pollution. In contrast, pig fecal pollution might account for the prevalence of tetO. Moreover, combined human-pig fecal pollution contributed to the observed bla_NDM-1 distribution in the Longjiang watershed. Subsequent analysis of the characteristics of MST markers disclosed that the relatively lower specificities of BacHum and Rum-2-Bac may lead to inaccurate results of tracking ARG pollution source. The present study determined spatiotemporal variations and ARG origins in the Longjiang watershed by combining MST markers. It also underscored the necessity of using multiple MST markers simultaneously to identify and characterize ARG pollution sources accurately.

Distribution of human fecal marker genes and their association with pathogenic viruses in untreated wastewater determined using quantitative PCR

Quantitative microbial risk assessment (QMRA) of human health risks using human fecal marker genes (HFMGs) is an useful water quality management tool. To inform accurate QMRA analysis, generation of probability distribution functions for HFMGs, and reference pathogenic viruses can be improved by input of correlation and ratios based upon measurement of HFMGs and gene copies (GC) of pathogenic viruses in untreated wastewater. The concentrations of four HFMGs (Bacteroides HF183, Lachnospiraceae Lachno3, CrAssphage and pepper mild mottle virus (PMMoV)), and GC of three reference pathogenic viruses human adenovirus 40/41 (HAdV 40/41), human norovirus GI + GII HNoV GI + GII and enterovirus (EV) were measured in untreated wastewater samples collected over a period of 12 months from two wastewater treatment plants in Sydney, Australia using quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR). Over the course of the study, the GC of potential pathogenic viruses were 3-5 orders of magnitude lower than HFMGs in untreated wastewater. The GC of pathogenic viruses were highly variable over the course of the study, which contrasted with the concentrations of HFMGs that were quite stable with little variation observed within and between WWTPs. Among the HFMGs, HF183, CrAssphage and PMMoV correlated well with pathogenic virus GC, whereas weak or negative correlations were observed between Lachno3 and pathogenic virus GC. While the two assessed WWTPs had dissimilar population service sizes, the ratios between log₁₀ transformed pathogenic virus GC and HFMGs demonstrated similar central tendency and variability for the same combinations between WWTP A and WWTP B with no difference between the WWTPs. This suggests the widespread presence of these HFMGs in both populations serviced by these two WWTPs. The observed correlation and ratios of HFMGs and GC of reference pathogenic viruses can contribute to improved QMRA of human health risks in environmental waters subject to fresh sewer overflows.

Effective coastal Escherichia coli monitoring by unmanned aerial vehicles (UAV) thermal infrared images

Coastal Escherichia coli (E. coli) significantly influence ocean safety and public health, thus requiring an effective E. coli pollution monitoring. However conventional detection relying on manual field sampling is time-consuming. Here, this study established an E. coli estimation model based on thermal remote sensing of unmanned aerial vehicles (UAV). This model was developed against one-year comprehensive field work in a representative sandy beach and further validated against 50 beaches in Hong Kong to evaluate its applicability. The estimated E. coli concentrations were in a reliable agreement with direct measurements. For this model, this study deployed the radon-222 (²²²Rn) as a bridging tracer to couple UAV thermal images and coastal E. coli concentrations. Coastal ²²²Rn can be reflected on the UAV thermal images, and there was a good positive correlation between the ²²²Rn activity and coastal E. coli concentration via one-year field data. Hence, coupling the ²²²Rn activity estimated from UAV thermal images and the relationship between ²²²Rn and E. coli, this study can readily monitor coastal E. coli by UAV. These findings highlighted that UAV technology is an effective approach to measure the E. coli concentrations and can further pave the way for an efficient coastal E. coli monitoring and public health risk warning.

Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters

Antibiotic resistance is a global threat to human health. Many surface water resources are environmental hotspots of antibiotic resistant gene (ARG) transfer, with agricultural runoff and human waste highlighted as common sources of ARGs to aquatic systems. Here we quantified fecal marker genes and ARGs in 992 stream water samples collected seasonally during a 5-year period from 115 sites across the Upper Oconee watershed (Georgia, USA), an area characterized by gradients of agricultural and urban development. Widespread fecal contamination was found from humans (48% of samples), ruminants (55%), and poultry (19%), and 73% of samples tested positive for at least one of the six targeted ARGs (ermB, tet(B), bla_CTX-M-1, bla_KPC, bla_SHV, and qnrS). While ARGs were strongly correlated with human fecal markers, many highly contaminated samples were not associated with sewage outfalls, an expected source of fecal and ARG pollution. To determine sources of contamination, we synthesized ARG and fecal marker data with geospatial data on land use/land cover and wastewater infrastructure across the watershed. This novel analysis found strong correlations between ARGs and measures of sewer density, sewer length, and septic system age within sample watersheds, indicating non-point sources of fecal contamination from aging wastewater infrastructure can be critical disseminators of anthropogenic ARGs in the environment.

Tracking bacterial pollution at a marine wastewater outfall site - A case study from Norway

Coastal marine environments are increasingly affected by anthropogenic impacts, such as the release of sewage at outfall sites and agricultural run-off. Fecal pollution introduced to the sea through these activities poses risks of spreading microbial diseases and disseminating antibiotic resistant bacteria and their genes. The study area of this research, Bore beach, is situated between two such point sources, an outfall site where treated sewage is released 1 km off the coast and a stream that carries run-off from an agricultural area to the northern end of the beach. In order to investigate whether and to what extent fecal contamination from the sewage outfall reached the beach, we used microbial source tracking, based on whole community analysis. Samples were collected from sea water at varying distances from the sewage outfall site and along the beach, as well as from the sewage effluent and the stream. Amplicon sequencing of 16S rRNA genes from all the collected samples was carried out at two time points (June and September). In addition, the seawater at the sewage outfall site and the sewage effluent were subject to shotgun metagenomics. To estimate the contribution of the sewage effluent and the stream to the microbial communities at Bore beach, we employed SourceTracker2, a program that uses a Bayesian algorithm to perform such quantification. The SourceTracker2 results suggested that the sewage effluent is likely to spread fecal contamination towards the beach to a greater extent than anticipated based on the prevailing sea current. The estimated mixing proportions of sewage at the near-beach site (P4) were 0.22 and 0.035% in June and September, respectively. This was somewhat below that stream's contribution in June (0.028%) and 10-fold higher than the stream's contribution in September (0.004%). Our analysis identified a sewage signal in all the tested seawater samples.

Sterols and sterol ratios to trace fecal contamination: pitfalls and potential solutions

Fecal pollution in surface waters is a major threat to recreational and drinking water resources, with Escherichia coli being a primary concern. The best way to mitigate fecal pollutant loading is to identify the sources and tailor remediation strategies to reduce loading. Tracking E. coli back to its source is notoriously difficult in a mixed-use watershed where input from humans, wildlife, and livestock all contribute to E. coli loading. One proposed tracking method for E. coli contamination is the use of fecal sterols and sterol ratios. This study uses fecal sterol data published globally to assess how well sterol compositions for different species clusters along with the effectiveness of sterol ratios as tracking tools. Hierarchical cluster analysis produces stronger clusters based on sterol ratios than raw sterol concentration, but the global dataset results in clustering of the same species in different levels. The accuracy of the sterol ratios was also compared to understand the rate of false negatives and false positive assignments. Overall, these ratios did not have a high success rate for determining the correct source, which was also reflected in the poor clustering trends observed. Establishing local end-member sterol profiles is essential when using sterol signatures to unravel fecal loading.

Geochemical characterization and health risk assessment in two diversified environmental settings (Southern Italy)

An integrated approach using chemical and microbial indicators has been tested in two different sites of the Campania Plain (Southern Italy) with different land use covering and different hydrogeological features in order: (1) to define the water-rock interaction processes, (2) to differentiate sources of pollution in a detailed way (3) to evaluate the degree of water quality in the studied alluvial aquifer and (4) to identify the most worrying elements for human's health. Groundwater have showed a HCO₃-Ca signature for both investigated sites, and a progressive enrichment in alkali ions has been highlighted moving from the boundary of the plain toward the coastal areas, due to groundwater interaction with volcanic rocks along the flow path. The application of the Factor Analysis allowed to identify different sources of pollution, which were attributed to (a) leaks in the sewer system for the Agro-Aversano Area and also the spreading of manure as fertilizers in agricultural activities for the Caiazzo Plain. Furthermore, it has been highlighted that the use of major elements, trace elements and microbiological indicators, allows to accurately differentiate contamination processes in progress. In fact, from the results of the Factor Analysis applied in the Agro-Aversano area, no significant statistically relationships between major elements and microbiological indicators of fecal contamination were highlighted, unlike the Caiazzo plain where statistically significant correlations have been found between major and trace elements and microbiological indicators. The use of a Groundwater Quality Index has shown general poor water quality for the majority of analyzed samples due to the high amount of Nitrate and Fecal indicators. The use of a Health Risk Assessment highlighted that Nitrate coupled with Fluoride represent the most important concern for human health compared to the all investigated parameters in both sites.

Connecting microbial, nutrient, physiochemical, and land use variables for the evaluation of water quality within mixed use watersheds

As non-point sources of pollution begin to overtake point sources in watersheds, source identification and complicating variables such as rainfall are growing in importance. Microbial source tracking (MST) allows for identification of fecal contamination sources in watersheds; when combined with data on land use and co-occuring variables (e.g., nutrients, sediment runoff) MST can provide a basis for understanding how to effectively remediate water quality. To determine spatial and temporal trends in microbial contamination and correlations between MST and nutrients, water samples (n = 136) were collected between April 2017 and May of 2018 during eight sampling events from 17 sites in 5 mixed-use watersheds. These samples were analyzed for three MST markers (human - B. theta; bovine - CowM2; porcine - Pig2Bac) along with E. coli, nutrients (nitrogen and phosphorus species), and physiochemical paramaters. These water quality variables were then paired with data on land use, streamflow, precipitation and management practices (e.g., tile drainage, septic tank density, tillage practices) to determine if any significant relationships existed between the observed microbial contamination and these variables. The porcine marker was the only marker that was highly correlated (p value <0.05) with nitrogen and phosphorus species in multiple clustering schemes. Significant relationships were also identified between MST markers and variables that demonstrated temporal trends driven by precipitation and spatial trends driven by septic tanks and management practices (tillage and drainage) when spatial clustering was employed.

Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese

Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10^-4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.

Fecal indicator organisms in northern oligotrophic rivers: An explorative study on Escherichia coli prevalence in a mountain region with intense tourism and reindeer herding

Increasing pollution levels in waters from remote mountain areas in northern Sweden have been observed. To support a sustainable water quality management, it is necessary to know which environmental and antrophogenic factors influence the water quality. The purpose of this study was to map the Escherichia coli prevalence in the catchment area of the upper part of a large northern Scandinavian river and investigate the controlling factors of microbial contamination. A total of 112 water samples were collected from various locations in the research area between July 2020 and December 2020. These samples were analyzed for microbial and chemical characteristics, and information about tourism and reindeer herding was compiled. Additionally, microbial and physicochemical water characteristics collected by Indalsälven Water Conservation Association (IWCA, 1993-2020) and Swedish Meteorological and Hydrological Institute (SMHI, 2004-2020) were analyzed. The results showed that E. coli enumerations ranged between 0 and 500 CFU/100 ml. There was generally no obvious relation between suspected point sources, e.g., sewage treatment plants at mountain stations, and E. coli levels at downstream sampling points. Principal component analysis showed that E. coli was correlated to coliforms, total heterotrophic count, river discharge, COD_Mn and river color. Since microbial analyses are time-consuming, expensive and difficult to perform in remote areas, it is important to find more easily extracted water parameters that can serve as a proxy for E. coli. In particular, river color and discharge are promising parameters that may serve as an early indication of bacterial outbreak and fecal contamination in mountain waters.

Modeling human pollution in water bodies using somatic coliphages and bacteriophages that infect Bacteroides thetaiotaomicron strain GA17

The ability to detect human fecal pollution in water is of great importance when assessing the associated health risks. Many microbial source tracking (MST) markers have been proposed to determine the origin of fecal pollution, but their application remains challenging. A range of factors, not yet sufficiently analyzed, may affect MST markers in the environment, such as dilution and inactivation processes. In this work, a statistical framework based on Monte Carlo simulations and non-linear regression was used to develop a classification procedure for use in MST studies. The predictive model tested uses only two parameters: somatic coliphages (SOMCPH), as an index of general fecal pollution, and human host-specific bacteriophages that infect Bacteroides thetaiotaomicron strain GA17 (GA17PH). Taking into account bacteriophage dilution and differential inactivation, the threshold concentration of SOMCPH was calculated to be around 500 PFU/100 mL for a limit of detection of 10 PFU/100 mL. However, this threshold can be lowered by increasing the analyzed volume sample, which in turn lowers the limit of detection. The resulting model is sufficiently accurate for application in practical cases involving MST and could be easily used with markers other than those tested here.

Co-occurrence of crAssphage and antibiotic resistance genes in agricultural soils of the Yangtze River Delta, China

Agricultural soil is highly susceptible to manure contamination and thus is a potential source for the spread of pathogens and antibiotic resistance genes (ARGs). Routine monitoring fecal contamination in agricultural soil can reduce the manure-derived ARG contaminations. This study investigated the distribution of crAssphage, a highly human-specific indicator of fecal pollution, in agricultural soils in the Yangtze River Delta (YRD) of China, and its potential in serving as an indicator of soil ARGs. CrAssphage was indeed strongly correlated with the abundance of soil ARGs, and particularly tetracycline resistance gene tetW (rho = 0.55, p < 0.01). Meanwhile, with the increasing of crAssphage abundance, the frequency of multiple abundant ARGs is also increased. When the relative abundance of crAssphage in soil samples exceeded 4.94 × 10^-4 copies per copy of the 16S rRNA gene, there would be more than three types of co-existing ARGs. Regional differences in crAssphage and ARGs abundances were observed for samples collected from Zhejiang, Shanghai, Jiangsu, and Anhui in the YRD, indicating different levels of fecal pollution therein. High sewage treatment capacity could contribute to the reduce of fecal pollution and the control ARG transmission in agricultural soils.

Persisting antibiotic resistance gene pollution and its association with human sewage sources in tropical marine beach waters

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are pollutants of worldwide concern that threaten human health and ecosystems. Anthropogenic activities and wastewater could be ARB and ARG pollution sources; however, research on ARG abundance and microbial source tracking (MST) of contamination in tropical marine waters is limited. This study examined spatiotemporal variations of six ARGs (bla_NDM, bla_TEM, bla_VIM, mcr-1, sul1, and tetQ) against the widely used antibiotic groups and a class 1 integron-integrase gene (intI1) at two Thai tropical recreational beaches (n = 41). Correlations between ARGs and sewage-specific MST markers (i.e., crAssphage and human polyomaviruses [HPyVs]) and fecal indicator bacteria (i.e., total coliforms, fecal coliforms, and enterococci) were also investigated. Bla_TEM, intI1, sul1, and tetQ were ubiquitous at both beaches (85.4-100% detection rate); intI1 was the most abundant (3-6 orders in log₁₀ copies/100 mL), followed by bla_TEM (2-4 orders), sul1 (2-3 orders), and tetQ (2-4 orders). Bla_NDM was found in 7.3% (up to 4 orders), and no mcr-1 was detected. Interestingly, bla_VIM was prevalent at one beach (2-5 orders; n = 17), but found in only one sample at the other (4 orders). Temporal, but not spatial, differences were noticed; bla_TEM was at higher levels in the wet season. IntI1 correlated with sul1 and tetQ (Spearman's rho = 0.47-0.97), suggesting potential horizontal gene transfer. CrAssphage, but not HPyVs, correlated with intI1, sul1, and tetQ (Spearman's rho = 0.50-0.74). Higher numbers of ARGs tended to co-occur in samples with higher crAssphage concentrations, implying sewage contribution to the marine water, with a persisting ARG background. This study provides insight into the ARG pollution status of tropical coastal waters and suggests crAssphage as a proxy for ARG pollution, which could facilitate effective management policies to minimize ARG dissemination in marine environments.

Effect of temperature on the persistence of fecal bacteria in ambient anaerobic digestion systems treating swine manure

This study aimed to explore the effect of temperature on the persistence of fecal bacteria by multiple approaches in ambient anaerobic digestion systems treating swine manure. Both lab-scale (15 °C, 20 °C, and 25 °C) and field (26 °C on average) studies were conducted by high-throughput sequencing and culture-based methods. A community-wide Bayesian SourceTracker method was used to identify and estimate the fecal bacterial proportion in anaerobic effluent. High proportional contributions of fecal bacteria were observed in effluent at 15 °C (73%) and 20 °C (75%), while less was found at 25 °C (19%). This was further verified by a field study (23%) and an anaerobic reactor study at 37 °C (0.01%). To explore the potential reasons for differences in fecal bacterial proportions, bacterial taxa were divided into "lost" and "survivor" taxa in manure waste by LEfSe. The "survivor" taxa abundance was positively correlated with SourceTracker proportion (r = 0.913, P = 0.001), but negatively correlated with temperature (r = -0.826, P = 0.006). In addition, biomarkers in effluent were divided into "enriched" and "de novo" taxa. "Enriched" taxa, including acidogenic and acetogenic bacteria, were found at all temperatures, whereas taxa related to organic degradation were multiplied "de novo" at 25 °C. Variation partition analysis showed that temperature could explain 30% of variations in effluent bacterial community. Moreover, coliforms isolated from the manure and effluents at 15 °C and 20 °C were also phylogenetically related. This study provided comprehensive insight into the impact of temperature on the persistence of fecal bacteria in anaerobic effluent, with temperatures over 25 °C recommended to reduce fecal pollution.

Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China

Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.

Occurrence of Giardia duodenalis in selected stations and tributary rivers of Laguna Lake, Philippines

Fecal pollution is a major contributor to the progressive degradation of Laguna Lake, the Philippines' largest inland lake used for aquaculture, recreation, and as a source of irrigation and domestic water. Consequently, intestinal parasites may be present in this body of water, posing risks to water safety and human health. This study was able to detect the protozoan parasite, Giardia duodenalis, in three Laguna Lake stations and seven tributary rivers in a 13-month monitoring period by PCR amplification of the small subunit ribosomal RNA (SSU rRNA) gene of Giardia cysts concentrated from water samples. The pathogen was present in 37.7% of tributary samples (n = 69) and 16.7% of lake samples (n = 36). Notable frequencies of detection were observed in four tributary rivers -Bagumbayan, Taguig (66.7%); Santa Rosa, Laguna (55.6%); San Cristobal, Cabuyao, Laguna (44.4%); and Biñan, Laguna (42.9%). All test SSU rRNA gene sequences were identified as human-infective genotypes of G. duodenalis predominated by Assemblage A (94.1%). Furthermore, analysis of the glutamate dehydrogenase (gdh) gene revealed the possible presence of mixed genotypes in at least two samples. These results support the pressing need to include protozoan pathogen monitoring in Laguna Lake and its tributaries to prevent Giardia infection in humans and animals. This study also recommends microbial source tracking to identify fecal pollution sources and aid in regulation of waste discharges into the lake and its tributaries.

Long-term water quality analysis reveals correlation between bacterial pollution and sea level rise in the northwestern Gulf of Mexico

Long-term assessments are needed to identify water quality trends and their socio-environmental drivers for coastal management and watershed restoration. This study provides the first long-term assessment of fecal bacterial pollution in the northwestern Gulf of Mexico using enterococci data spanning the Texas coast from 2009 to 2020. The data were representative of 66 beaches, 169 stations, and over 75,000 samples. Findings demonstrate that 22 beaches are 'hotspots' of pollution and experienced enterococci levels that frequently exceeded the USEPA beach action value. Further, enterococci were correlated with time, population size, and sea level. Weak correlations detected in some counties highlight the multifactorial nature of water quality; additional factors are likely influencing enterococci levels. The correlation with sea level is concerning, as counties vulnerable to sea level rise frequently reported enterococci concentrations exceeding the beach action value. In consideration of sea level rise predictions, targeted studies are needed to pinpoint drivers of fecal pollution.

Identification of new eligible indicator organisms for combined sewer overflow via 16S rRNA gene amplicon sequencing in Kanda River, Tokyo

Fecal indicator bacteria (FIB) are commonly used to evaluate the pollution impact of combined sewer overflows (CSOs) in urban rivers. Although water quality assessment with FIB has a long tradition, recent studies demonstrated that FIB have a low correlation with pathogens and therefore are not accurate enough for the assessment of potential human hazards in water. Consequently, new eligible and more specific indicators have to be identified, which was done in this study via sequencing of genetic markers from total community DNA. To identify potential microbiome-based indicators, microbial communities in samples from an urban river in Tokyo under different climatic conditions (dry and rainy) were compared with the influent and effluent of three domestic wastewater treatment plants (WWTPs) by analyzing 16 S rRNA gene amplicon libraries. In the first part of this study, physicochemical parameters and FIB quantification with selective culture techniques facilitated the identification of samples contaminated with CSO, sewage, or both. This allowed the grouping of samples into CSO-contaminated and non-contaminated samples, an essential step prior to the microbiome comparison between samples. Increased turbidity, ammonia concentrations, and E. coli [up to (9.37 ± 0.95) × 10² CFU/mL after 11.5 mm of rainfall] were observed in CSO-contaminated river samples. Comparison of dry weather (including WWTP samples) and rainy weather samples showed a reduction in microbial diversity in CSO-contaminated samples. Furthermore, the results of this study suggest Bacteroides spp. as a novel indicator of sewage pollution in surface waters.

Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand

Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log₁₀ copies/100 mL), crAssphage (5.28-7.38 log₁₀ copies/100 mL), and HPyVs (3.66-6.53 log₁₀ copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log₁₀ copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log₁₀ copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log₁₀ copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log₁₀ copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.

CrAssphage for fecal source tracking in Chile: Covariation with norovirus, HF183, and bacterial indicators

Anthropogenic fecal pollution in urban waterbodies can promote the spread of waterborne disease. The objective of this study was to test crAssphage, a novel viral human fecal marker not previously applied for fecal source tracking in Latin America, as a fecal pollution marker in an urban river in Chile. Human fecal markers crAssphage CPQ_064 and Bacteroides HF183, the human pathogen norovirus GII, and culturable fecal indicator bacteria (FIB) were quantified at six locations spanning reaches of the Mapocho River from upstream to downstream of Santiago, as well as in repeated sub-daily frequency samples at two urban locations. Norovirus showed positive correlation trends with crAssphage (τ = 0.57, p = 0.06) and HF183 (τ = 0.64, p = 0.03) in river water, but not with E. coli or enterococci. CrAssphage and HF183 concentrations were strongly linearly related (slope = 0.97, p < 0.001). Chlorinated wastewater effluent was an important source of norovirus GII genes to the Mapocho. Precipitation showed non-significant positive relationships with human and general fecal indicators. Concentrations of crAssphage and HF183 in untreated sewage were 8.35 and 8.07 log₁₀ copy/100 ml, respectively. Preliminary specificity testing did not detect crAssphage or HF183 in bird or dog feces, which are predominant non-human fecal sources in the urban Mapocho watershed. This study is the first to test crAssphage for microbial source tracking in Latin America, provides insight into fecal pollution dynamics in a highly engineered natural system, and indicates river reaches where exposure to human fecal pollution may pose a public health risk.

F-specific coliphage detection by the Bluephage method

F-specific coliphages have been proposed as viral indicators of fecal pollution. These intestinal phages infect cells through the F-pili of the host strains used for their detection, Escherichia. coli HS/FAmp in the US-EPA standard method and Salmonella enterica WG49 in the ISO method. The recently designed Bluephage protocol allows the rapid detection of as low as one somatic coliphage in a working day. The current study describes a new Bluephage method designed to exclusively detect F-specific phages. It employs two new host strains, CB14 and CB16, which detect the same number of F-specific phages as their respective parental strains HS and WG49. In the Bluephage method, when the strain is lysed by bacteriophage infection, the yellow medium turns blue. As low as one F-specific phage was detected in 3 to 5 h by this approach and when the sample contained high phage concentrations, results were obtained in less than 3 h. The F-specific Bluephage method can be used with different sample volumes and allows phage quantification by the most probable number technique. Strain CB14 performed more consistently than CB16, with comparable detection efficiency after increasing the incubation time to 50 min without shaking.

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer

The Edwards Aquifer serves as a primary source of drinking water to more than 2 million people in south-central Texas, and as a karst aquifer, is vulnerable to human and animal fecal contamination which poses a serious risk to human and environmental health. A one-year study (Jan 2018 - Feb 2019) was conducted to determine the primary sources of fecal pollution along the Balcones and Leon Creek within the Edwards Aquifer recharge and contributing zones using general (E. coli, enterococci, and universal Bacteriodales) and host-associated (human-, dog-, cow- and chicken/duck-associated Bacteriodales) microbial source tracking (MST) assays. Additionally, sites were classified based on surrounding land use as a potential source predictor and marker levels were correlated with rain events and water quality parameters. Levels for the three general indicators were highest and exhibited similar trends across the sampling sites, suggesting that the sole use of these markers is not sufficient for specific fecal source identification. Among the host-associated markers, highest concentrations were observed for the dog marker (BacCan) in the Leon Creek area and the cow marker (BacCow) in the Balcones Creek area. Additionally, Chicken/Duck-Bac, BacCan and BacCow all exhibited higher concentrations during the spring season and the end of fall/early winter. Relatively lower concentrations were observed for the human-associated markers (HF183 and BacHum), however, levels were higher in the Leon Creek area and highest following rainfall events. Additionally, relatively higher levels in HF183 and BacHum were observed at sites having greater human population and septic tank density and may be attributed to leaks or breaks in these infrastructures. This study is the first to examine and compare fecal contamination at rural and urban areas in the recharge and contributing zones of the Edwards Aquifer using a molecular MST approach targeting Bacteroidales 16S rRNA gene-based assays. The Bacteroidales marker assays, when combined with land use and weather information, can allow for a better understanding of the sources and fluxes of fecal contamination, which can help devise effective mitigation measures to protect water quality.

Elucidating fecal pollution patterns in alluvial water resources by linking standard fecal indicator bacteria to river connectivity and genetic microbial source tracking

A novel concept for fecal pollution analysis was applied at alluvial water resources to substantially extend the information provided by fecal indicator bacteria (FIB). FIB data were linked to river connectivity and genetic microbial source tracking (MST). The concept was demonstrated at the Danube River and its associated backwater area downstream of the city of Vienna, using a comprehensive 3-year data set (10 selected sites, n = 317 samples). Enumeration of Escherichia coli (ISO 16649-2), intestinal enterococci (ISO 7899-2) and Clostridium perfringens (ISO 14189) revealed a patchy distribution for the investigation area. Based on these parameters alone a clear interpretation of the observed fecal contamination patterns was not possible. Comparison of FIB concentrations to river connectivity allowed defining sites with dominating versus rare fecal pollution influence from the River Danube. A strong connectivity gradient at the selected backwater sites became obvious by 2D hydrodynamic surface water modeling, ranging from 278 days (25%) down to 5 days (<1%) of hydraulic connectivity to the River Danube within the 3-year study period. Human sewage pollution could be identified as the dominating fecal source at the highly connected sites by adding information from MST analysis. In contrast, animal fecal pollution proofed to be dominating in areas with low river connectivity. The selection of genetic MST markers was focusing on potentially important pollution sources in the backwater area, using human (BacHum, HF183II), ruminant (BacR) and pig (Pig2Bac) -associated quantitative PCR assays. The presented approach is assumed to be useful to characterize alluvial water resources for water safety management throughout the globe, by allocating fecal pollution to autochthonous, allochthonous, human or animal contamination components. The established river connectivity metric is not limited to bacterial fecal pollution, but can be applied to any type of chemical and microbiological contamination.

Implementation and integration of microbial source tracking in a river watershed monitoring plan

Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess their usefulness as an effective management tool of water quality. First, the potential of the selected markers to track the source was evaluated using fresh fecal samples. Subsequently, we evaluated their performance in a catchment with different impacts, considering land use and environmental conditions. All MST markers showed high sensitivity and specificity, although none achieved 100% for both. Although some of the MST markers were detected in hosts other than the intended ones, their abundance in the target group was always several orders of magnitude higher than in the non-target hosts, demonstrating their suitability to distinguish between sources of pollution. The MST analysis matched the land use in the watershed allowing an accurate assessment of the main sources of pollution, in this case mainly human and ruminant pollution. Correlating environmental parameters including temperature and rainfall with MST markers provided insight into the dynamics of the pollution in the catchment. The levels of the human marker showed a significant negative correlation with rainfall in human polluted areas suggesting a dilution of the pollution, whereas at agricultural areas the ruminant marker increased with rainfall. There were no seasonal differences in the levels of human marker, indicating human pollution as a constant pressure throughout the year, whereas the levels of the ruminant marker was influenced by the seasons, being more abundant in summer and autumn. MST analysis integrated with land use and environmental data can improve the management of fecal polluted areas and set up best practice.

Microbial source tracking (MST) in Chattahoochee River National Recreation Area: Seasonal and precipitation trends in MST marker concentrations, and associations with E. coli levels, pathogenic marker presence, and land use

Escherichia coli levels in recreational waters are often used to predict when fecal-associated pathogen levels are a human health risk. The reach of the Chattahoochee River that flows through the Chattahoochee River National Recreation Area (CRNRA), located in the Atlanta-metropolitan area, is a popular recreation area that frequently exceeds the U.S. Environmental Protection Agency beach action value (BAV) for E. coli. A BacteriALERT program has been implemented to provide real-time E. coli estimates in the reach and notify the public of potentially harmful levels of fecal-associated pathogens as indicated by surrogate models based on real-time turbidity measurements from continuous water quality monitoring stations. However, E. coli does not provide information about the sources of fecal contamination and its accuracy as a human health indicator is questionable when sources of contamination are non-human. The objectives of our study were to investigate, within the Park and surrounding watersheds, seasonal and precipitation-related patterns in microbial source tracking marker concentrations of possible sources (human, dog, and ruminant), assess correlations between source contamination levels and culturable E. coli levels, determine which sources best explained model-based E. coli estimates above the BAV and detection of esp2 (a marker for the esp gene associated with pathogenic strains of Enterococcus faecium and Enterococcus faecalis), and investigate associations between source contamination levels and land use features. Three BacteriALERT sites on the Chattahoochee River were sampled six times per season in the winter and summer from December 2015 through September 2017, and 11 additional stream sites (synoptic sites) from the CRNRA watershed were sampled once per season. Samples were screened with microbial source tracking (MST) quantitative PCR (qPCR) markers for humans (HF183 Taqman), dogs (DogBact), and ruminants (Rum2Bac), the esp2 qPCR marker, and culturable E. coli. At the BacteriALERT sites, HF183 Taqman concentrations were higher under wet conditions DogBact concentrations were greater in the winter and under wet conditions, and Rum2Bac concentrations were comparatively low throughout the study with no difference across seasons or precipitation conditions. Concentrations of HF183 Taqman, DogBact, and Rum2Bac were positively correlated with culturable E. coli concentrations; however, DogBact had the largest R² value among the three markers, and the forward stepwise regression indicated it was the best predictor of culturable E. coli concentrations at the BacteriALERT sites. Recursive partitioning indicated that BAV exceedances of model-based E. coli estimates were best explained by DogBact concentrations ≥3 gene copies per mL (CN/mL). Detections of esp2 at BacteriALERT sites were best explained by DogBact concentrations ≥11 CN/mL, while detections of esp2 at synoptic sites were best explained by HF183 Taqman ≥29 CN/mL. At the synoptic sites, HF183 Taqman levels were associated with wastewater treatment plant density. However, this relationship was driven primarily by a single site, suggesting possible conveyance issues in that catchment. esp2 detections at synoptic sites were positively associated with development within a 2-km radius and negatively associated with development within the catchment, suggesting multiple sources of esp2 in the watershed. DogBact and Rum2Bac were not associated with the land use features included in our analyses. Implications for Park management include: 1) fecal contamination levels were highest during wet conditions and in the off season when fewer visitors are expected to be participating in water-based recreation, 2) dogs are likely contributors to fecal contamination in the CRNRA and may be sources of pathogenic bacteria indicating further investigation of the origins of this contamination may be warranted as would be research to understand the human health risks from exposure to dog fecal contamination, and 3) high levels of the human marker at one site in the CRNRA watershed suggests more extensive monitoring in that catchment may locate the origin of human fecal contamination detected during this study.

Response of prokaryotic communities to extreme precipitation events in an urban coastal lagoon: A case study of Yundang lagoon, China

Increasing extreme precipitation events (EPEs) can induce biogeochemical disturbances in the coastal lagoon ecosystems. Very little is known about the response of prokaryotic communities to such influences, which are the key components mediating the biogeochemical cycling in lagoons. Here 16S rRNA gene amplicon sequencing and high-through quantitative PCR (HT-qPCR) were employed to investigate the distribution of prokaryotic communities and fecal indicator genes in the surface waters of Yundang lagoon, Xiamen, China during EPEs, respectively. Prokaryotic communities from rainwaters, influents (IFs) and effluents (EFs) from a nearby wastewater treatment plant were also characterised. The results indicated a significant variation in the composition of lagoon prokaryotic communities compared with rainwaters, IFs and EFs. Multivariate and phylogenetic signal analyses revealed that environmental filtering, mainly controlled by salinity, was the major ecological process responsible for the temporal succession of lagoon prokaryotic communities during EPEs. Moreover, the pollution indicator taxa (based on amplicon sequencing) and fecal indicator genes (based on HT-qPCR) demonstrated that EPEs may induce sewage overflows and fecal pollution (mainly from humans and dogs), resulting in an increase in the relative abundance of pollution indicator taxa and genes in Yundang lagoon. Network analysis illustrated that the number of network edges and keystone species decreased along the sampling times, implying that EPEs-induced disturbances may affect prokaryotic species associations. Taken together, this study provides an enhanced understanding of the responses of lagoon prokaryotic communities to EPEs-induced disturbances.

Fecal pollution source tracking and thalassogenic diseases: The temporal-spatial concordance between maximum concentrations of human mitochondrial DNA in seawater and Hepatitis A outbreaks among a coastal population

Fecal pollution source tracking (FST) studies the origin of fecal contamination and promotes action to eliminate it to improve human health and environmental sustainability. This work presents the temporal and spatial relations of human mitochondrial DNA (HmtDNA), fecal coliforms (FC) and live microbial biomass (ATP) in seawater during a hepatitis A outbreak among a human coastal population. The study area is approximately 100 km along the coastline of the Biobío Region in the southeastern Pacific (Humboldt Current System, Chile). Total data from the swash zone from summer 2015 to autumn 2016 show there were significant positive log-log correlations between FC and HmtDNA (R = 0.32) and ATP (R = 0.31). These correlations were highest during the austral spring of 2015 (R = 0.53 and 0.58 respectively), when HmtDNA also correlated significantly with ATP (R = 0.86). Maximum average values of the parameters measured in this season showed a temporal-spatial concordance with the peak in the number of hepatitis A cases among the nearby coastal population. FC correlated significantly with HmtDNA (R = 0.98) in the water column of the coastal zone close to Concepción Bay during the austral summer of 2016 and in the swash zone of the bay (R = 0.68) throughout the study period. Hepatitis A virus (HAV) has also been detected in organisms and seawater in Concepción Bay, which is consistent with the high incidence of hepatitis A among the coastal population. The concordance between human fecal pollution in the study area and a seasonal hepatitis A outbreak strongly suggests that HmtDNA and its relation with FC and ATP in the coastal zone of marine environments can be used as a proxy to evaluate the risk of outbreaks of thalassogenic diseases.

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.

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

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

Marker genes of fecal indicator bacteria and potential pathogens in animal feces in subtropical catchments

We investigated the abundance of marker genes of two fecal indicator bacteria (FIB) and eight potential pathogens in fecal samples of humans (n = 14) and 10 domestic and native wild animals (n = 134). For each target animal, between 10 and 14 individual fecal samples were collected (n = 148 individual fecal samples in total). The abundance of FIB and potential pathogens within each sample was determined using quantitative PCR (qPCR) assays. All animals tested were positive for Escherichia coli (EC) and the concentrations ranged from 6.13 (flying fox) to 8.87 (chicken) log₁₀ GC/g of feces. These values for Enterococcus spp. (ENT) were 5.25 log₁₀ GC/g for flying fox and 8.12 log₁₀ GC/g of feces for chicken. Moderate correlations were observed between EC with P. aeruginosa, EC O157 and Cryptosporidium parvum, whereas weak correlations were observed between EC and Salmonella spp. and Giardia lamblia, Mycobacterium avium complex (MAC) and Campylobacter spp. The prevalence of MAC and P. aeruginosa were low in dog (14.3% each) and moderate (57.2%, MAC; 42.9% P. aeruginosa) in Eastern grey kangaroo fecal samples. Cryptosporidium parvum was detected in one cattle and one human fecal sample, while G. lamblia was detected in one dog, one flying fox, and one pig fecal samples. Among the eight potential pathogens tested, five pathogens were detected in chicken and dog fecal samples. The remaining animal species contained up to three potential pathogens in their feces. The data generated in this study may aid in the calculation of pathogen loads in the environment, and hence to assess the risks from human and animal fecal contamination of source waters.

New approach for the simultaneous detection of somatic coliphages and F-specific RNA coliphages as indicators of fecal pollution

Two groups of coliphages have been recently included in different water management policies as indicators of viral fecal pollution in water and food: somatic coliphages, which infect E. coli through cell wall receptors, and F-specific RNA coliphages, which infect through the F-pili. Somatic coliphages are more abundant in fecally contaminated waters, except reclaimed waters, those disinfected by UV irradiation, and some groundwater samples that show a higher level of F-specific coliphages. Somatic coliphages are morphologically similar to DNA enteric viruses while F-specific coliphages are similar to RNA viruses such as norovirus and hepatitis A viruses, which are the viral pathogens of concern in sewage. The use of strains sensitive to both types of phages has been proposed for total coliphage enumeration, thereby avoiding double analysis. The standardized methods available for coliphage detection are robust and cost-effective, but the introduction of ready-to-use methods would facilitate routine implementation in laboratories. The fastest available tool for somatic coliphage enumeration is the recently developed Bluephage, which uses a modified β-glucuronide-overexpressing E. coli strain unable to take up the glucuronide substrate. The overexpressed enzyme accumulates inside the bacterial cells until released by phage-induced cell lysis, whereupon it encounters its substrate and the medium changes from yellow to blue. The present method uses E. coli strain CB12, sensitive to somatic coliphages and F-specific coliphages due to the expression of the F-pili. The Bluephage approach incorporating CB12 detects both types of coliphages in a time range of 1:30 to 4:00 h, as assayed with coliphages from raw sewage, river water, sludge and mussels. This strategy can be applied to obtain qualitative and quantitative results and is applicable to microplates as well as to large sample volumes (100 ml). Moreover it can provide monitoring of water bodies at real time, as for example for ambient recreational beach monitoring.

Spatial patterns of enzymatic activity in large water bodies: Ship-borne measurements of beta-D-glucuronidase activity as a rapid indicator of microbial water quality

This study used automated enzymatic activity measurements conducted from a mobile research vessel to detect the spatial variability of beta‑d‑glucuronidase (GLUC) activity in large freshwater bodies. The ship-borne observations provided the first high-resolution spatial data of GLUC activity in large water bodies as rapid indication of fecal pollution and were used to identify associations with hydrological conditions and land use. The utility of this novel approach for water quality screening was evaluated by surveys of the Columbia River, the Mississippi River and the Yahara Lakes, covering up to a 500 km river course and 50 km² lake area. The ship-borne measurements of GLUC activity correlated with standard E. coli analyses (R² = 0.71) and revealed the effects of (1) precipitation events and urban run-off on GLUC activity in surface waters, (2) localized point inlets of potential fecal pollution and (3) increasing GLUC signals along gradients of urbanization. We propose that this ship-borne water quality screening to be integrated into future water inventory programs as an initial or complementary tool (besides established fecal indicator parameters), due to its ability to provide near real-time spatial information on potential fecal contamination of large surface water resources and therefore being helpful to greatly reduce potential human health risks.

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

An enteric virus surrogate and reliable domestic wastewater tracer is needed to manage microbial quality of food and water as (waste)water reuse becomes more prevalent in response to population growth, urbanization, and climate change. Pepper mild mottle virus (PMMoV), a plant pathogen found at high concentrations in domestic wastewater, is a promising surrogate for enteric viruses that has been incorporated into over 29 water- and food-related microbial quality and technology investigations around the world. This review consolidates the available literature from across disciplines to provide guidance on the utility of PMMoV as either an enteric virus surrogate and/or domestic wastewater marker in various situations. Synthesis of the available research supports PMMoV as a useful enteric virus process indicator since its high concentrations in source water allow for identifying the extent of virus log-reductions in field, pilot, and full-scale (waste)water treatment systems. PMMoV reduction levels during many forms of wastewater treatment were less than or equal to the reduction of other viruses, suggesting this virus can serve as an enteric virus surrogate when evaluating new treatment technologies. PMMoV excels as an index virus for enteric viruses in environmental waters exposed to untreated domestic wastewater because it was detected more frequently and in higher concentrations than other human viruses in groundwater (72.2%) and surface waters (freshwater, 94.5% and coastal, 72.2%), with pathogen co-detection rates as high as 72.3%. Additionally, PMMoV is an important microbial source tracking marker, most appropriately associated with untreated domestic wastewater, where its pooled-specificity is 90% and pooled-sensitivity is 100%, as opposed to human feces where its pooled-sensitivity is only 11.3%. A limited number of studies have also suggested that PMMoV may be a useful index virus for enteric viruses in monitoring the microbial quality of fresh produce and shellfish, but further research is needed on these topics. Finally, future work is needed to fill in knowledge gaps regarding PMMoV's global specificity and sensitivity.

PCR data and comparative performance of Bacteroidales microbial source tracking genetic markers

We reported modified endpoint PCR results analyzed by universal and human-, swine-, and cattle-specific Bacteroidales gene markers with human sewage and animal fecal samples (i.e., swine, cattle, chicken, goat, sheep, buffalo, and duck) from Tha Chin and Chao Phraya watersheds. Annealing locations of PCR primers were illustrated by maps of 16s rRNA Bacteroidales genes. We also summarized previously published work on the performance of the PCR assays. For further discussion of the data presented here, please refer to Somnark et al., Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds, Environ. Pollut. 236 (2018) 100–110.

Evaluation of the novel crAssphage marker for sewage pollution tracking in storm drain outfalls in Tampa, Florida

CrAssphage are recently-discovered DNA bacteriophages that are prevalent and abundant in human feces and sewage. We assessed the performance characteristics of a crAssphage quantitative PCR (qPCR) assay for quantifying sewage impacts in stormwater and surface water in subtropical Tampa, Florida. The mean concentrations of crAssphage in untreated sewage ranged from 9.08 to 9.98 log₁₀ gene copies/L. Specificity was 0.927 against 83 non-human fecal reference samples and the sensitivity was 1.0. Cross-reactivity was observed in DNA extracted from soiled poultry litter but the concentrations were substantially lower than untreated sewage. The presence of the crAssphage marker was monitored in water samples from storm drain outfalls during dry and wet weather conditions in Tampa, Florida. In dry weather conditions, 41.6% of storm drain outfalls samples were positive for the crAssphage marker and the concentrations ranged from 3.60 to 4.65 log₁₀ gene copies/L of water. After a significant rain event, 66.6% of stormwater outlet samples were positive for the crAssphage marker and the concentration ranged from 3.62 to 4.91 log₁₀ gene copies/L of water. The presence of the most commonly used Bacteroides HF183 marker in storm drain outfalls was also tested along with the crAssphage. Thirteen samples (55%) were either positive (i.e., both markers were present) or negative (i.e., both markers were absent) for both the markers. Due to the observed cross-reactivity of this marker with DNA extracted from poultry litter samples, it is recommended that this marker should be used in conjunction with additional markers such as HF183. Our data indicate that the crAssphage marker is highly sensitive to sewage, is adequately specific, and will be a valuable addition to the MST toolbox.

Potential for gulls to transport bacteria from human waste sites to beaches

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape.

Development and small-scale validation of a novel pigeon-associated mitochondrial DNA source tracking marker for the detection of fecal contamination in harvested rainwater

The current study was aimed at designing and validating (on a small-scale) a novel pigeon mitochondrial DNA (mtDNA) microbial source tracking (MST) marker for the detection of pigeon fecal matter in harvested rainwater. The pigeon mtDNA MST marker was designed to target the mtDNA Cytochrome b gene by employing mismatch amplification mutation assay kinetics. The pigeon marker was validated by screening 69 non-pigeon and 9 pigeon fecal samples. The host-sensitivity of the assay was determined as 1.00 while the host-specificity of the assay was 0.96. Harvested rainwater samples (n=60) were screened for the prevalence of the marker with the mtDNA Cytochrome b marker detected in 78% of the samples. Bayes' theorem was applied to calculate the conditional probability of the marker detecting true pigeon contamination and the marker subsequently displayed a 99% probability of detecting true pigeon contamination in the harvested rainwater samples. In addition, the mtDNA Cytochrome b marker displayed high concurrence frequencies versus heterotrophic bacteria (78.3%), E. coli (73.3%), total coliforms (71.1%) and fecal coliforms (66.7%). This study thus validates that targeting mtDNA for the design of source tracking markers may be a valuable tool to detect avian fecal contamination in environmental waters.

Bluephage: A rapid method for the detection of somatic coliphages used as indicators of fecal pollution in water

The use of somatic coliphages as indicators of fecal and viral pollution in water and food has great potential due to the reliability, reproducibility, speed and cost effectiveness of methods for their detection. Indeed, several countries already use this approach in their water management policies. Although standardized protocols for somatic coliphage detection are available, user-friendly commercial kits would facilitate their routine implementation in laboratories. The new method presented here allows detection of up to 1 somatic coliphage in under 3.5 h, well within one working day. The method is based on a modified Escherichia coli strain with knocked-out uidB and uidC genes, which encode the transport of glucuronic acid inside cells, and overexpressing uidA, which encodes the enzyme β-glucuronidase. The enzyme accumulated in the bacterial cells only has contact with its substrate after cell lysis, such as that caused by phages, since the strain cannot internalize the substrate. When the enzyme is released into the medium, which contains a chromogen analogous to glucuronic acid, it produces a change of color from yellow to dark blue. This microbiological method for the determination of fecal pollution via the detection of culturable microorganisms can be applied to diverse sample types and volumes for qualitative (presence/absence) and quantitative analysis and is the fastest reported to date.

Urban sewage lipids in the suspended particulate matter of a coral reef under river influence in the South West Gulf of Mexico

Nutritional quality of suspended particulate matter (SPM) and the degree of human fecal pollution in the largest coral reef system in the southwest Gulf of Mexico were evaluated using lipid classes, fatty acids (FA) and sterols in the dry and rainy seasons. High proportions of triacylglycerols and saturated and monounsaturated FA were detected in the SPM however it was considered poor quality because it had low proportions of highly unsaturated FA which can be used to determine production of marine biogenic material of dietary value to pelagic and benthic organisms. Urban sewage organic carbon was traced with coprostanol. The reference value of coprostanol from the point source of pollution was set using two samples from a sewage treatment plant processing waste from >140,000 people near the coral reef system, and it was contrasted with one river station and nine marine stations including six coral reefs. The concentration of coprostanol in the SPM was 3621 ± 98 ng L^-1 comprising 26% of total sterols. During the dry season, the river was contaminated upstream with human feces as evidenced by coprostanol at 1823 ng L^-1, the 5β-coprostanol: cholesterol ratio at 0.5, and 5β-coprostanol: [5α-cholestanol+5β-coprostanol] at 0.7. In contrast, marine stations had concentrations of coprostanol lower than a suggested regulation limit for tropical marine coastal waters (30 ng L^-1), ranging between 6 and 28 ng L^-1. During the rainy season a dilution effect was detected in the river, however significantly higher concentrations of coprostanol in the marine stations were detected ranging between 15 and 215 ng L^-1, higher than the tentative tropical regulation range (30-100 ng L^-1). Among the reefs, the nearshore one, 14.3 km from the treatment plant, was more exposed to human-fecal pollution, and offshore reefs, >17.3 km from the plant, had a lower degree of contamination. Finally, only three stations were clearly uncontaminated during both seasons including two reefs in the south located 21.8 and 35.6 km from the plant, with no presence of coprostanol. Contamination in the rainy season likely comes from a village with untreated sewage located 9.3-32 km from the reefs, and from the second largest Mexican river flowing into the Gulf of Mexico which has a watershed covering three states with lower than average sewage treatment. Inclusion of coprostanol monitoring could be a key factor in the management of this coral reef system.

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

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