Baseline and storm event monitoring of Bacteroidales marker concentrations and enteric pathogen presence in a rural Canadian watershed

Widespread occurrence of fecal indicator bacteria in oligotrophic tropical streams. Are common culture-based coliform tests appropriate?

Monitoring of stream water quality is a key element of water resource management worldwide, but methods that are commonly used in temperate habitats may not be appropriate in humid tropical systems. We assessed the influence of four land uses on microbial water quality in 21 streams in the Panama Canal Watershed over a one-year period, using a common culture-based fecal indicator test and 16S rDNA metabarcoding. Each stream was located within one of four land uses: mature forest, secondary forest, silvopasture, and traditional cattle pasture. Culturing detected total coliforms and Escherichia coli across all sites but found no significant differences in concentrations between land uses. However, 16S rDNA metabarcoding revealed variability in the abundance of coliforms across land uses and several genera that can cause false positives in culture-based tests. Our results indicate that culture-based fecal indicator bacteria tests targeting coliforms may be poor indicators of fecal contamination in Neotropical oligotrophic streams and suggest that tests targeting members of the Bacteroidales would provide a more reliable indication of fecal contamination.

Using isotopic tracers to enhance routine watershed monitoring - Insights from an intensively managed agricultural catchment

Experimental (research-based) and non-research-based watershed monitoring programs often differ with respect to sampling frequency, monitored variables, and monitoring objectives. Isotopic variables, which are more commonly incorporated in research-based programs, can provide an indication of water sources and the transit time of water in a catchment. These variables may be a valuable complement to traditional water quality monitoring variables and have the potential to support improved hydrologic process-related insights from long term monitoring programs that typically have low resolution sampling. The purpose of this investigation is to explore the utility of incorporating isotopic variables (specifically δ18O, δ2H, and 222Rn) into routine monthly sampling regimes by comparing insights gained from these variables to monitoring only specific conductivity and chloride. A complete annual cycle of monthly groundwater and surface water monitoring data collected from the Upper Parkhill watershed in southwestern Ontario, Canada was used to characterize baseline watershed conditions, evaluate watershed resilience to climate change, and examine contamination vulnerability. Study results provide an improved understanding of appropriate tracer use in agricultural regions with isotopic variables able to provide important insights into the seasonality of hydrologic phenomena, such as the timing of groundwater recharge. A comparison of monitoring variables to present-day hydro-meteorological conditions suggests the importance of a winter dominated hydrologic regime and the potential influence of changes in precipitation on groundwater-surface water interactions. Estimated transit time dynamics indicate the likelihood for rapid contaminant transport through surface and shallow subsurface flow and highlight the possible effects of agricultural tile drainage. The sampling approach and data analysis methods adopted in this study provide the basis for improving routine watershed monitoring programs in agricultural regions.

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.

Chemical and biological tracers to identify source and transport pathways of septic system contamination to streams in areas with low permeability soils

Septic systems are widely used in rural areas that lack centralized sewage treatment systems. Incomplete removal of domestic wastewater contaminants in septic systems can lead to leaching of nutrients (P and N), bacteria/viruses, and trace contaminants to surrounding groundwater and surface water. This study focuses on delineating the fate of wastewater contaminants in localities where septic systems are installed in moderate to fine-grained overburden materials to assess potential impacts on groundwater and surface water quality in these settings. Nutrients and a suite of anthropogenic tracers, including host-specific fecal indicator bacteria (bovine- and human-specific Bacteroides), pharmaceutical compounds (caffeine, carbamazepine, gemfibrozil, ibuprofen, naproxen, and sulfamethoxazole), and an artificial sweetener (acesulfame-K), were selected to evaluate differences in transport properties. Surface water samples (n = 103) were collected from streams upstream (US) and downstream (DS) of three rural hamlets up to two times monthly over one year. Results indicate the presence of wastewater indicators in the streams, with DS locations showing significantly elevated concentrations of both chemical and biological anthropogenic tracers. Human-specific Bacteroides, caffeine, and acesulfame-K were consistently observed at elevated concentrations at all DS sites. Nutrients exhibited varied concentrations between US and DS locations at three study sites. The occurrence of human-specific Bacteroides in the surface water samples suggests the presence of preferential flow pathways within the silt/clay overburden. These results demonstrate the advantages of using a combined tracer approach, involving a conservative tracer such as acesulfame-K coupled with the human-specific biological indicator Bacteroides (BacHum), to understand not only impacting sources but also potential transport pathways of septic system contamination to nearby streams. Septic systems may be an underappreciated contaminant source in rural hamlets located in fine-grained overburden materials; although, a distinction of specific nutrient sources (septic systems vs. agriculture) remains challenging.

Fecal pollution source characterization in the surface waters of recharge and contributing zones of a karst aquifer using general and host-associated fecal genetic markers

Fecal pollution of surface waters in the karst-dominated Edwards aquifer is a serious concern as contaminated waters can rapidly transmit to groundwaters, which are used for domestic purposes. Although microbial source tracking (MST) detects sources of fecal pollution, integrating data related to environmental processes (precipitation) and land management practices (septic tanks) with MST can provide better understanding of fecal contamination fluxes to implement effective mitigation strategies. Here, we investigated fecal sources and their spatial origins at recharge and contributing zones of the Edwards aquifer and identified their relationship with nutrients in different environmental/land-use conditions. During March 2019 to March 2020, water samples (n = 295) were collected biweekly from 11 sampling sites across four creeks and analyzed for six physico-chemical parameters and ten fecal indicator bacteria (FIB) and MST-based qPCR assays targeting general (E. coli, Enterococcus, and universal Bacteroidales), human (BacHum and HF183), ruminant (Rum2Bac), cattle (BacCow), canine (BacCan), and avian (Chicken/Duck-Bac and GFD) fecal markers. Among physico-chemical parameters, nitrate-N (NO₃-N) concentrations at several sites were higher than estimated national background concentrations for streams. General fecal markers were detected in the majority of water samples, and among host-associated MST markers, GFD, BacCow, and Rum2Bac were more frequently detected than BacCan, BacHum, and HF183, indicating avian and ruminant fecal contamination is a major concern. Cluster analysis results indicated that sampling sites clustered based on precipitation and septic tank density showed significant correlation (p < 0.05) between nutrients and FIB/MST markers, indicating these factors are influencing the spatial and temporal variations of fecal sources. Overall, results emphasize that integration of environmental/land-use data with MST is crucial for a better understanding of nutrient loading and fecal contamination.

Composition-oriented estimation of biogas production from major culinary wastes in an anaerobic bioreactor and its associated CO2 reduction potential

Despite the wide applications of dry anaerobic digestion (AD), a number of fundamental issues, such as composition-oriented estimation of biogas production and CO₂ reduction potential, were not well understood yet. The objective of this study was to establish composition-oriented models for prediction of biogas production and the associated shift of microbial communities. Three important factors regarding feedstock, including loading, carbon-to-nitrogen ratio, and solid-to-liquid ratio, were found to significantly affect the biogas production. The biogas production and digestion kinetics were evaluated with the response surface methodology. The major contribution to biogas production was found to be hydrogenotrophic methanogens (82.6 ± 0.4%). The net CO₂ reduction potential was assessed from the life-cycle approach, and a substantial amount of CO₂ generation (i.e., 2.8-6.7 tonne/tonne-VS) could be reduced by AD, compared to incineration, revealing that dry AD for food waste treatment should be one of the essential practices in the portfolio of global CO₂ mitigation.

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.

Different micro-aeration rates facilitate production of different end-products from source-diverted blackwater

The effects of micro-aeration on the performance of anaerobic sequencing batch reactors (ASBR) for blackwater treatment were investigated in this study. Different micro-aeration rates, 0, 5, 10, 50, and 150 mg O₂/L-reactor/cycle, and their effect on the hydrolysis, acidogenesis, and methanogenesis of blackwater were evaluated and compared at ambient temperature. Source-diverted blackwater (toilet water) contains high organic contents which can be recovered as biogas. Previous studies have found that anaerobic digestion of blackwater without micro-aeration can only recover upwards of less than 40% of chemical oxygen demand (COD) to methane at room temperature due to the low hydrolysis rate of biomass content in blackwater. This study achieved increases in blackwater hydrolysis (from 34.7% to 48.7%) and methane production (from 39.6% to 50.7%) with controlled micro-aeration (5 mg O₂/L-reactor/cycle). The microbial analysis results showed that hydrolytic/fermentative bacteria and acetoclastic methanogens (e.g. Methanosaeta) were in higher abundances in low-dose micro-aeration reactors (5 and 10 mg O₂/L-reactor/cycle), which facilitated syntrophic interactions between microorganisms. The relative abundance of oxygen-tolerant methanogen such as Methanosarcina greatly increased (from 1.5% to 11.4%) after oxygen injection. High oxygen dosages (50 and 150 mg O₂/L-reactor/cycle) led to reduced methane production and higher accumulation of volatile fatty acids, largely due to the oxygen inhibition on methanogens and degradation of organic matters by aerobic growth and respiration, as indicated by the predicted metagenome functions. By combining reactor performance results and microbial community analyses, this study demonstrated that low-dose micro-aeration improves blackwater biomethane recovery by enhancing hydrolysis efficiency and promoting the development of a functional microbial population, while medium to high-dose micro-aeration reduced the activities of certain anaerobes. It was also observed that medium-dose micro-aeration maximizes VFA accumulation, which may be used in two-stage anaerobic digesters.

Rainfall-driven E. coli transfer to the stream-conduit network observed through increasing spatial scales in mixed land-use paddy farming karst terrain

Karst aquifers have distinctive hydrology and supply 25% of the world's population with drinking water, making them a critical geological setting for understanding and managing microbial water pollution. Rainfall causes elevated concentrations and loading of faecal microorganisms, e.g. E. coli, in catchment surface and groundwater systems, increasing the risk of human exposure to faecally-contaminated water. However, effective management of microbial water quality in complex karst catchments is constrained by limited understanding of E. coli - discharge responses to rainfall. We analysed how rainfall events of varying magnitude (2.4-100 mm) control E. coli-discharge dynamics at increasing spatial scales in a mixed land-use karst catchment in southwest China. During the wet season, hourly water sampling was undertaken throughout five storm events to characterise in high detail E. coli emergence with resulting flow across multiple sites of varying catchment area, stream order, and land-use. E. coli concentration was found to increase by 1-3 orders of magnitude following rainfall events. Maximum E. coli concentration and speed of E. coli recession were influenced by rainfall (amount, intensity), timing of agricultural activities, and position in the hydrological system. For high intensity events ∼90% of the cumulative E. coli export occurred within 48 h. E. coli concentration increased with increasing discharge at all sites. E. coli concentration at low discharge was higher in the headwaters than at the catchment outlet, while the rate of increase in E. coli concentration with increasing discharge appears to follow the opposite trend, being higher at the catchment outlet than the headwaters. This was attributed to the decreasing flow path gradient and increasing degree of development of the fissure network, but further event monitoring at varying catchment scales is required to confirm this relationship. The results provide novel insight into how rainfall characteristics combine with land-use and catchment hydrology to control E. coli export in karst landscapes.

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

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

Relationships between chemical and microbial faecal source tracking markers in urban river water and sediments during and post-discharge of human sewage

This study explores the relationships between faecal source tracking (FST) markers (quantitative Polymerase Chain Reaction (qPCR) markers and steroids), microbial indicators, the faecal ageing ratio of atypical colonies/total coliforms (AC/TC) and potential human pathogens (Giardia, Cryptosporidium and Campylobacter). Faecal source PCR markers tested were GenBac3, HumM3, HumBac (HF183-Bac708R); Bifidobacterium adolescentis, wildfowl and canine-associated markers. Sediment and water samples from the Avon River were collected during and post-discharge of untreated human sewage inputs, following a series of earthquakes, which severely damaged the Christchurch sewerage system. Significant, positive Spearman Ranks (r_s) correlations were observed between human-associated qPCR markers and steroid FST markers and Escherichia coli and F-specific RNA bacteriophage (r_s 0.57 to 0.84, p < 0.001) in water samples. These human source indicative FST markers demonstrated that they were also effective predictors of potentially pathogenic protozoa in water (r_s 0.43-0.74, p ≤ 0.002), but correlated less well with Campylobacter. Human-associated qPCR and steroid markers showed significant, substantial agreement between the two FST methods (Cohen's kappa, 0.78, p = 0.023), suggesting that water managers could be confident in the results using either method under these contamination conditions. Low levels of fluorescent whitening agents (FWA) (mean 0.06 μg/L, range 0.01-0.40 μg/L) were observed in water throughout the study, but steroids and FWA appeared to be retained in river sediments, months after continuous sewage discharges had ceased. No relationship was observed between chemical FST markers in sediments and the overlying water, and few correlations in sediment between chemical FST markers and target microorganisms. The low values observed for the faecal ageing ratio, AC/TC in water, were significantly, negatively correlated with increasing pathogen detection. This study provides support for the use of the AC/TC ratio, and qPCR and steroid FST markers as indicators of health risks associated with the discharge of raw human sewage into a freshwater system.

Quantitative assessment of Naegleria fowleri and fecal indicator bacteria in brackish water of Lake Pontchartrain, Louisiana

Brackish water samples from Lake Pontchartrain in Louisiana were assessed for the presence of pathogenic amoeba Naegleria fowleri, which causes primary amoebic meningoencephalitis (PAM). In our study, quantitative polymerase chain reaction (qPCR) methods were used to determine N. fowleri, E. coli, and enterococci in water collected from Lake Pontchartrain. N. fowleri target sequence was detected in 35.4% (56/158) of the water samples from ten sites around the lake. Statistically significant positive correlations between N. fowleri concentration and water temperature as well as E. coli (qPCR) were observed. Multiple linear regression (MLR) model shows seasonal factor (summer or winter) has significant effect on the concentration of N. fowleri, E. coli and enterococci (qPCR) concentration. Significant positive relationships between E. coli and enterococci was observed from both qPCR (r=0.25) and culture based method (r=0.54). Meanwhile, significant positive correlation between qPCR and culture based methods for enterococci concentration was observed (r=0.33). In our study, water temperature and E. coli concentration were indicative of N. fowleri concentrations in brackish water environment. Future research is needed to determine whether sediment is a source of N. fowleri found in the water column.

Assessment of fecal pollution in Lake Pontchartrain, Louisiana

Water quality in Lake Pontchartrain was deteriorating and recreational activities along the beach were restricted by the end of the 20th Century. A microbial source tracking (MST) study was conducted to determine the fecal contamination sources at public beach of the lake, so that effective pollution control strategies can be developed. Water samples were collected over an eight-month period at ten locations along the lake in 2016 and 2017. E. coli and Enterococcus were detected in 90.6% (culture) and 97.5% (qPCR), 95.8% (culture) and 91.8% (qPCR) of water samples from all sampling sites, respectively. Significant positive relationship between E. coli and Enterococcus results was observed for both qPCR and culture methods. HF183 marker was detected in 94.3% water samples (149 of 158), with concentrations ranging from 29.0 to 6073.5GC/100ml and from 129.8 to 38,465.6GC/100ml in summer and winter, respectively. The results also indicate that significant rainfall events have the potential to supply considerable loads of fecal bacteria to lake waters. Further research is needed to determine the contribution of other animals to fecal contamination in the region.

Temporal variation in the prevalence and species richness of Campylobacter spp. in a prairie watershed impacted by urban and agricultural mixed inputs

Campylobacter spp. are a substantial cause of gastroenteritis worldwide. Human infection can result from ingestion of contaminated food or water from a variety of sources, including the consumption of fresh produce that is contaminated with the pathogen via the use of contaminated irrigation water. Using molecular methods, we investigated the occurrence of Campylobacter in the Qu’Appelle River watershed, an important source of irrigation water for vegetable producers in southern Saskatchewan, Canada. Water samples were collected from 7 sampling sites from April to September 2009 (145 samples), and from 5 sampling sites from May to October 2013 (116 samples). Campylobacter was detected in 57% and 16% of the samples collected in 2009 and 2013, respectively. Campylobacter detection was highest in May and June for both sampling years. In 2009, the predominant species were Campylobacter lari and Campylobacter jejuni, with prevalences of 84% and 41%, respectively. Other Campylobacter spp. were detected less frequently. Only C. lari was detected in 2013. The results in 2009 demonstrate the species richness of Campylobacter in water sources within the watershed. The occurrence of Campylobacter in the study area also underscores the importance of monitoring irrigation water used to irrigate fresh produce from a public health prospective.

Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution

This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml(-1)) and biologically treated wastewater samples (median log10 6.2-6.5 ME 100 ml(-1)), irrespective of plant size, type and time of the season (n = 53-65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3-3.0) and treated wastewater (s* = 3.7-4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support if highly specific markers are needed.