Microbial Water Quality Assessment Research Articles

To gate or not to gate: Revisiting drinking water microbial assessment through flow cytometry fingerprinting

Flow cytometry has been utilized for over a decade as a rapid and reproducible approach to assessing microbial quality of drinking water. However, the need for specialized expertise in gating—a fundamental strategy for distinguishing cell populations—introduces the potential for human error and obstructs the standardization of methods. This work conducts a comprehensive analysis of various gating approaches applied to flow cytometric scatter plots, using a dataset spanning a year. A sensitivity analysis is carried out to examine the impact of different gating strategies on final cell count results. The findings show that dynamic gating, which requires user intervention, is essential for the analysis of highly variable raw waters and distributed water. In contrast, static gating proved suitable for more stable water sources, interstage sample locations, and water presenting a particularly low cell count. Our conclusions suggest that cell count analysis should be supplemented with fluorescence fingerprinting to gain a more complete understanding of the variability in microbial populations within drinking water supplies. Establishing dynamic baselines for each water type in FCM monitoring studies is essential for choosing the correct gating strategy. FCM fingerprinting offers a dynamic approach to quantify treatment processes, enabling options for much better monitoring and control. This study offers new insights into the vagaries of various flow cytometry gating strategies, thereby substantially contributing to best practices in the water industry. The findings foster more efficient and reliable water analysis, improving of standardizing methods in microbial water quality assessment using FCM.

Global microbial water quality data and predictive analytics: Key to health and meeting SDG 6

Microbial water quality is an integral to water security and is directly linked to human health, food safety, and ecosystem services. However, specifically pathogen data and even faecal indicator data (e.g., E. coli), are sparse and scattered, and their availability in different water bodies (e.g., groundwater) and in different socio-economic contexts (e.g., low- and middle-income countries) are inequitable. There is an urgent need to assess and collate microbial data across the world to evaluate the global state of ambient water quality, water treatment, and health risk, as time is running out to meet Sustainable Development Goal (SDG) 6 by 2030. The overall goal of this paper is to illustrate the need and advocate for building a robust and useful microbial water quality database and consortium worldwide that will help achieve SDG 6. We summarize available data and existing databases on microbial water quality, discuss methods for producing new data on microbial water quality, and identify models and analytical tools that utilize microbial data to support decision making. This review identified global datasets (7 databases), and regional datasets for Africa (3 databases), Australia/New Zealand (6 databases), Asia (3 databases), Europe (7 databases), North America (12 databases) and South America (1 database). Data are missing for low- and middle-income countries. Increased laboratory capacity (due to COVID-19 pandemic) and molecular tools can identify potential pollution sources and monitor directly for pathogens. Models and analytical tools can support microbial water quality assessment by making geospatial and temporal inferences where data are lacking. A genomics, information technology (IT), and data revolution is upon us and presents unprecedented opportunities to develop software and devices for real-time logging, automated analysis, standardization, and modelling of microbial data to strengthen knowledge of global water quality. These opportunities should be leveraged for achieving SDG 6 around the world.

Microbial Source Tracking: An Emerging Technology for Microbial Water Quality Assessment: A Review

Microbial Source Tracking is a scientific approach that primarily aims to identify the sources of faecal contamination in water bodies. Microbial Source Tracking (MST) is a set of techniques employed to identify the origins of faecal contamination in water. The capacity to track faecal bacteria to their source is a crucial aspect of both public health and water quality management. The utilisation of information obtained from the method of MST would provide water quality managers with an enhanced comprehension of the origins of contamination, thus facilitating the implementation of remedial measures to impede transmission. Numerous studies have demonstrated that the gut-associated bacteria of the order Bacteroidales, specifically the Bacteroides genus, has a tendency to undergo co-evolution with the host, making it a highly viable option for MST applications. However, it is noteworthy that MST is also facilitating the scientific community with effective techniques for tracing faecal bacteria and pathogens in water sources. The methodologies utilised in MST are frequently categorised as either Library-Dependent Methods (LDMs) or Library-Independent Methods (LIMs). Microbial source tracking has been employed for diverse objectives, such as ensuring adherence to regulations, remediating pollution, and evaluating risk. The implementation of MST is expected to mitigate the prevalence of waterborne illnesses resulting from contamination. The implementation of MST has facilitated the ability to anticipate the probable origins of faecal contamination and the associated health hazards linked to compromised water systems. In addition to conventional faecal indicators, these methodologies are suggested as means to furnish supplementary insights into the origins of pollution, as well as the ecological and public health ramifications of animal-derived water contamination. 

Microbial Water Quality Assessment of Private Wells Using 16S rRNA Gene Amplicon Sequencing with a Nanopore Sequencer.

Private wells are used daily worldwide as convenient household water sources. In Japan, where water supply coverage is high, well water is occasionally used for non-potable purposes, such as irrigation and watering. Currently, the main microbiological test of well water is designed to detect Escherichia coli, which is an indicator of fecal contamination, using culture methods. Water use such as watering generates bioaerosols, which may cause airborne infection. However, many causative bacteria of aerosol-derived infections, such as Legionella spp., are difficult to detect using culture methods. Thus, more comprehensive modern assessment is desirable for securing the microbiological quality of well water. Here, the bacterial community structure of five private wells located in different environments was examined using the rapid and portable MinION sequencer, which enabled us to identify bacteria to the species level based on full-length 16S ribosomal RNA (rRNA) gene sequences. The results revealed the differences in the bacterial community structures of water samples from the five wells and detected Legionella pneumophila and Aeromonas hydrophila as new candidate microbial indicators. The comprehensive analysis method used in this study successfully detected bacteria causing opportunistic infections, which are difficult to detect by conventional methods. This approach is expected to be routinely applied in the future as a highly accurate method for assessing the microbiological quality of private well water.

Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020–21 reveals widespread transcription of antibiotic resistance genes

Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR).Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 – August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed.To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.

PCR-based detection of pathogens in improved water sources: a scoping review protocol of the evidence in low-income and middle-income countries.

IntroductionOccurrence of diverse human enteric bacterial, viral and protozoal pathogens in improved drinking water because of pathogenic microbial contamination is of increasing public health concern, particularly in low-income and middle-income countries (LMICs). Detecting microbial pathogens in water supplies comprehensively and accurately is beneficial to ensure the safety of water in LMICs where water contamination is a major concern. Application of PCR-based methods in detecting the microbial quality of water provides more accurate, sensitive and rapid outcomes over conventional methods of microbial identification and quantification. Therefore, exploring water quality outcomes generated through PCR-based methods is important to better understand the status and monitor progress towards internationally set goals for LMICs. This scoping review aims to map the existing evidence on the magnitude and characteristics of diarrhoeagenic pathogens as detected by PCR-based methods in improved water sources within the context of LMICs.Methods and analysisThis study will be undertaken in line with the Joanna Briggs Institute (JBI) methodology for scoping reviews. We will consider the available publications covering PCR-based microbial water quality assessment of improved drinking water sources in LMICs. Searches will be undertaken in PubMed/Medline, Scopus, Web of Science, JBI, Cochrane Library and Google Scholar. A grey literature search will be conducted in Google and ProQuest.Ethics and disseminationThe College of Natural and Computational Science Institution Review Board of Addis Ababa University gave formal ethical approval to this study protocol. The findings of this study will be disseminated to the concerned body through peer-reviewed publications, presentations and summaries.

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Trends of recreational water quality in Albania’s coastal during 2016–2020

Water quality impairment is a substantial environmental hazard which impacts a wide variety of stakeholders and interests, particularly those who participate in outdoor water-based recreational activities. Recreational bathing water qualities are highly vulnerable to microbial pollution from municipal sewage, industrial effluents, agriculture run-off and river discharges. Fecal contamination impairs water quality and potentiates human health risks. The aim of this study was to see the 5-year trend of microbiological quality of recreational bathing waters in Albania. Every year we collected 1,071 samples taken 30 centimeters below the water’s surface at least one meter deep. Assessment of bacterial load of the coastal waters was done nine times for every point, for the Escherichia coli and Intestinal enterococci, according to the methods ISO 7899-1 and ISO 9308-3. Bathing water assessment is to be classified according the categories indicated in the Directive 2006/7/EC and recommendations of WHO/UNEP-2010. Microbial Water Quality Assessment Category (cfu/100 ml water) done in 119 monitoring points were: During 2016, Excellent 53%, Sufficient 23%, Good 9% and Poor 15%. In 2017, Excellent 68%, Sufficient 15%, Good 6% and Poor 10%. During 2018, Excellent 82.4%, Sufficient 13%, Good 0.9% and Poor 3.7%. During 2019, Excellent 89%, Sufficient 2.5%, Good 6% and Poor 2.5%. During 2020 Excellent 89.9%, Sufficient 5%, Good 0.9%, and Poor 4.2%. Based on the above assessment, it is noticed a significant increase of microbial quality of recreational bathing waters in Albania due to investments in the sewerage system and better waste water treatment.

Citizen science based monitoring of microbial water quality at a single household level in a South African local municipality during the COVID19 lockdown

Personal hygiene and access to potable water, which is safe for human consumption, are critical to containing the COVID19 pandemic. Here monitoring results are reported for microbial quality of water samples from the municipal supply in Makana Local Municipality in the Eastern Cape Province, South Africa. Access of the human population to sufficient volumes of potable water of required (microbial) quality has been a problem in this local municipality. Samples were taken just before and during 30 days of the strictest phase of the nation-wide lockdown, related to COVID19 in South Africa. Aim of this short communication was to perform the water quality testing with limited to no access to laboratory facilities and using the principles of citizen science. The H2S test kit was used as the basis for the microbial testing, while a cell phone app was used for the temperature monitoring. Five H2S test kit were used per sampling at the author’s house and the kits was developed for the microbial water quality assessment in isolated settings such as those for the lockdown. During the study, the ambient temperature ranged from 17 to 29 °C, with decreases below 18 °C occurring on three out of 12 sampling occasions. Thus the results of the H2S test kit might have been slightly influenced by the fluctuations of the ambient temperature. On 8 sampling occasions between 1 and 4 H2S test kits were positive for faecal contamination. Three samples or 25 % were free of faecal contamination. One sample had all five H2S test kits were positive for faecal contamination. Results of statistical testing indicated that potable water in Makana Local Municipality was probably microbially contaminated at the author’s household on an intermittent basis. Ongoing monitoring of microbial drinking water quality is necessary and continuing at the sampled location.

Effect of the time scale on the uncertainty of geometric mean concentrations of fecal indicators in creek under baseflow conditions

Geometric mean concentrations of fecal indicator bacteria E. coli and enterococci are commonly used to evaluate the microbial quality of irrigation, recreation, and other types of waters, as well in watershed-scale microbial water quality modeling. It is not known how the uncertainty of those geometric mean concentrations depends on the time period between sampling. We analyzed data collected under baseflow conditions from three years of weekly and several daily sampling campaigns at Conococheague Creek in Pennsylvania. Standard deviations of logarithms of geometric mean concentrations were computed over weeks, months, and seasons. The increase in standard deviations from weekly to seasonal time scale was on average about 0.1 and 0.2 for log(E. coli) and log(enterococci), respectively, and in most cases was statistically significant. This may need to be accounted for when evaluating the uncertainty of measurements for modeling purposes and in risk assessment of microbial water quality.

Microbial Water Quality Assessment of Packaged Drinking Water of Pre-School Children in some Parts of Accra

Episodes of Cholera outbreaks are still common in most developing countries and children usually are at the greatest risk. This study assessed the importance of diarrhoea-related illnesses among children five years of age or less at the University Hospital, Legon and the importance of packaged water handling in the contamination of drinking water of pre-school children. Diarrhea-related diseases (DRD) accounted for 6.3% of cases involving children five years and below reporting at the University Hospital, Legon during the period of the study. Generally, greater number of cases (DRD) were reported among males (6.9%) than among females (5.6%). High counts above recommended levels of either Total Heterotrophic Bacteria, Pseudomonas or Total Coliforms were observed in 88% of the water samples tested. Inadequate cleaning of water bottles and in some instances the use of inappropriate water bottles (reusing PET mineral water containers) contributed to the poor quality of the drinking water of the preschool children. A greater part of the contamination of the drinking water occurred at home and not at the schools. Parents therefore need to be targeted with water, sanitation and hygiene related health education.

Functional Evaluation of Three Manure-Borne Indicator Bacteria Release Models with Multiyear Field Experiment Data.

Modeling the fate and transport of Escherichia coli is of substantial interest because of how this organism serves as an indicator of fecal contamination in microbial water quality assessment. The efficacy of models used to assess the export of E. coli from agricultural fields is dependent, in part, on submodels they utilize to simulate E. coli release from land-applied manure and animal waste. Although several release submodels have been proposed, they have only been evaluated and compared with data from laboratory or small plot E. coli release experiments. Our objective was to evaluate and compare performances of three manure-borne bacteria release submodels at field-scale: exponential release (EM), two-parametric Bradford and Schijven (B-S), and two-parametric Vadas-Kleinman-Sharpley (VKS); each was independently incorporated and tested as a submodel within the export model KINEROS2/STWIR, using E. coli. Dairy manure was uniformly applied via surface broadcasting once a year for six consecutive years on a 0.28 ha experimental field site. Two irrigation events followed each application: the first immediately followed the initial application and the second occurred one week later. Manure and soil samples were collected before and after irrigation, respectively, and manure, soil, and edge-of-field runoff samples were analyzed for E. coli. Model performance was evaluated with the Akaike criterion, coefficients of determination (R2), and root mean squared errors (RMSE) values. The percentage of exported manure-borne E. coli varied from 0.1% to 10% in most cases, generally reflecting the lag time between initiation of irrigation and initiation ofedge-of-field runoff. The export model performed better when using the VKS submodel which was preferred in 55% of cases. The B-S and EM submodels were preferred in 27% and 18% of cases, respectively. Two-parametric submodels were ultimately preferred over the single parameter submodel.

Temporal Stability of Escherichia coli Concentrations in Waters of Two Irrigation Ponds in Maryland.

Fecal contamination of water sources is an important water quality issue for agricultural irrigation ponds. Escherichia coli concentrations are commonly used to evaluate recreational and irrigation water quality. We hypothesized that there may exist temporally stable spatial patterns of E. coli concentrations across ponds, meaning that some areas mostly have higher and other areas mostly lower than average concentrations of E. coli To test this hypothesis, we sampled two irrigation ponds in Maryland at nodes of spatial grids biweekly during the summer of 2016. Environmental covariates-temperature, turbidity, conductivity, pH, dissolved oxygen, chlorophyll a, and nutrients-were measured in conjunction with E. coli concentrations. Temporal stability was assessed using mean relative differences between measurements in each location and averaged measurements across ponds. Temporally stable spatial patterns of E. coli concentrations and the majority of environmental covariates were expressed for both ponds. In the pond interior, larger relative mean differences in chlorophyll a corresponded to smaller mean relative differences in E. coli concentrations, with a Spearman's rank correlation coefficient of 0.819. Turbidity and ammonium concentrations were the two other environmental covariates with the largest positive correlations between their location ranks and the E. coli concentration location ranks. Tenfold differences were found between geometric mean E. coli concentrations in locations that were consistently high or consistently low. The existence of temporally stable patterns of E. coli concentrations can affect the results of microbial water quality assessment in ponds and should be accounted for in microbial water quality monitoring design.IMPORTANCE The microbial quality of water in irrigation water sources must be assessed to prevent the spread of microbes that can cause disease in humans because of produce consumption. The microbial quality of irrigation water is evaluated based on concentrations of Escherichia coli as the indicator organism. Given the high spatial and temporal variability of E. coli concentrations in irrigation water sources, recommendations are needed on where and when samples of water have to be taken for microbial analysis. This work demonstrates the presence of a temporally stable spatial pattern in the distributions of E. coli concentrations across irrigation ponds. The ponds studied had zones where E. coli concentrations were mostly higher than average and zones where the concentrations were mostly lower than average over the entire observation period, covering the season when water was used for irrigation. Accounting for the existence of such zones will improve the design and implementation of microbial water quality monitoring.

Particle surface area and bacterial activity in recirculating aquaculture systems

Suspended particles in recirculating aquaculture systems (RAS) provide surface area that can be colonized by bacteria. More particles accumulate as the intensity of recirculation increases thus potentially increasing the bacterial carrying capacity of the systems. Applying a recent, rapid, culture-independent fluorometric detection method (Bactiquant®) for measuring bacterial activity, the current study explored the relationship between total particle surface area (TSA, derived from the size distribution of particles >5μm) and bacterial activity in freshwater RAS operated at increasing intensity of recirculation (feed loading from 0.043 to 3.13kgfeedm−3 make-up water). Four independent sets of water samples from different systems were analyzed and compared including samples from: (i) two individual constructed wetlands treating the effluent system water from two commercial, freshwater rainbow trout (Oncorhynchus mykiss) farms of different recirculation intensity; (ii) an 8.5m3 pilot scale RAS; and (iii) twelve identical, 1.7m3 pilot scale RAS assigned one of four micro-screen treatments (no micro-screen, 100, 60, or 20μm mesh size micro-screens) in triplicate. There was a strong, positive, linear correlation (p<0.05) between TSA and bacterial activity in all systems with low to moderate recirculation intensity (i.e. feed loading ≤1kgfeedm−3 make-up water). However, the relationship apparently ceased to exist in the systems with highest recirculation intensity (feed loading 3.13kg feedm−3 make-up water; corresponding to 0.32m3 make-upwaterkg−1 feed). This was likely due to the accumulation of dissolved nutrients sustaining free-living bacterial populations, and/or accumulation of suspended colloids and fine particles less than 5μm in diameter, which were not characterized in the study but may provide significant surface area. Hence, the study substantiates that particles in RAS provide surface area supporting bacterial activity, and that particles play a key role in controlling the bacterial carrying capacity at least in less intensive RAS. Applying fast, culture-independent techniques for determining bacterial activity might provide a means for future monitoring and assessment of microbial water quality in aquaculture farming systems.

Effect of Rainfall Events on the Microbial Quality of Recreational Water in the Swan and Canning Rivers in Western Australia

Background: Rainfall events are known to be associated with the health of recreational water. Pathogens in recreational water may pose a risk to bathers and water users, including naturally occurring microorganisms as well as those that are present as a result of faecal pollution. This study aims to investigate whether rainfall events impact on the microbial quality of recreational water in Swan Canning estuary in Western Australia (WA) and to identify and propose effective management interventions. Methods: Compliance of water quality in recreational waters is assessed according to microbial water quality assessment categories (MACs) based on the 95th percentile of enterococci counts with the use of Enterotester TemplateTM. Results: Results indicate that the number of enterococci in the water rises along with increasing volumes of rainfall. Enterococci levels between 201 to 500 MPN/100ml are associated with rainfall ranging from 3-21mm and elevated enterococci levels over 700 MPN/100ml are associated with rainfall ranging from 12-35mm. Conclusion: A causal relationship between enterococci levels in recreational waters and rainfall events exists. Enterococci levels increase following rainfall events of 5mm and over in the majority of sampling sites along the Swan and Canning Rivers during five consecutive bathing seasons. Although environmental and faecal pol- lutions also contribute to recreational water quality, summer rainfall data has indicated that recreational water bodies experience periods of increased enterococci levels as rainfall volumes increase. Keywords: Enterococci level, microbial assessment category, NHMRC guidelines, rainfall, recreational water, water quality.

Civic Engagement and Environmental Sustainability in Teaching and Learning at Higher Education Institution in South Africa

Abstract This article seeks to provide an outline the scope of professional teaching and learning activities and their connection to civic engagement and the achievement of environmental sustainability at Rhodes University and in Makana Local Municipality. Activities in the context of rainwater water harvesting and sanitation research are used as examples. The improved hydrogen-sulphide test kit was used as the tool for the assessment of microbial water quality between April and July 2016. An approach to the improvement in the design and modelling of the performance of ventillated improved pit latrines under laboratory conditions is also described. All activities described have been taking place in the context of undergraduate and postgraduate student research projects at Rhodes University. They have implications for teaching and learning, civic engagement and environmental sustainability. Teaching and learning of the concepts of sustainability can facilitate the development of the necessary connection between academia and the society at large. This can have a significant positive effect on societal conditions in South Africa. Further endeavours similar those described in this article should be stimulated in South and beyond.

Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation. The objective of this work was to evaluate the effect of interannual weather variability on surface water microbial quality. We used the Soil and Water Assessment Tool model to simulate E. coli concentrations in the Little Cove Creek; this is a perennial creek located in an agricultural watershed in south-eastern Pennsylvania. The model performance was evaluated using the US FDA regulatory microbial water quality metrics of geometric mean (GM) and the statistical threshold value (STV). Using the 90-year time series of weather observations, we simulated and randomly sampled the time series of E. coli concentrations. We found that weather conditions of a specific year may strongly affect the evaluation of microbial quality and that the long-term assessment of microbial water quality may be quite different from the evaluation based on short-term observations. The variations in microbial concentrations and water quality metrics were affected by location, wetness of the hydrological years, and seasonality, with 15.7–70.1% of samples exceeding the regulatory threshold. The results of this work demonstrate the value of using modeling to design and evaluate monitoring protocols to assess the microbial quality of water used for produce irrigation.

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

To what extent can portable fluorescence spectroscopy be used in the real-time assessment of microbial water quality?

The intrinsic fluorescence of aquatic organic matter emitted at 350nm when excited at 280nm correlates widely with water quality parameters such as biochemical oxygen demand. Hence, in sewage-impacted rivers and groundwater, it might be expected that fluorescence at these wavelengths will also correlate with the microbial water quality. In this paper we use a portable fluorimeter to assess the relationship between fluorescence intensity at this wavelength pair and Escherichia coli enumeration in contrasting river catchments of poor water quality: in KwaZulu-Natal, S. Africa and the West Midlands, UK. Across all catchments we demonstrate a log correlation (r=0.74) between fluorescence intensity and E. coli over a seven-log range in E. coli enumerations on non-perturbed (unfiltered) samples. Within specific catchments, the relationship between fluorescence intensity and E. coli is more variable, demonstrating the importance of catchment-specific interference. Our research demonstrates the potential of using a portable fluorimeter as an initial screening tool for indicative microbial water quality, and one that is ideally suited to simple pollution scenarios such as assessing the impact of faecal contamination in river or groundwater at specific sites.

Relationship between viral detection and turbidity in a watershed contaminated with group A rotavirus.

Enteric viruses are present in aquatic environments due to contamination by raw sewage, even in the absence of fecal coliforms, which are considered to be significant indicators when it comes to microbial water quality assessment. This study investigated the presence of group A rotavirus (RVA) in surface water from a river basin in Minas Gerais, Brazil, assessing the influence of the urbanization, the rainfall, and the microbiological and physico-chemical parameters regarding water quality. Forty-eight surface water samples collected in urbanized and non-urbanized areas, both in dry and rainy periods, were obtained throughout the study. The viral particles were concentrated by adsorption-elution in a negatively charged membrane. Fecal coliforms, as well as physico-chemical water parameters were determined at each point in all collections. The RVA was detected in 62.5 % (30/48) of the water samples through a real-time PCR assay. All the sequenced RVA strains belonged to genotype I1. The RVA was detected in 50.0 % (11/22) of the water samples regarded as being acceptable by current microbiological standards. The presence of the RVA and the viral load were influenced by the collection area (p < 0.05). It was also observed a significant association between the RVA and detecting the turbidity of water (p < 0.05). The collected data showed a high level of contamination in this watershed by the discharge of raw sewage, highlighting the need for urgent measures to improve water quality, ensuring the safe use of this matrix.