Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring

Preloading Long-Chain Quaternary Ammonium Groups to Synthesize a High-Efficient Anion-Exchange Resin for Eliminating Bacterial Contaminants in Drinking Water

Bacterial contamination in drinking water is a global health concern, necessitating the development of highly efficient treatment techniques. Anion-exchange resins (AERs) have long been employed for removing anionic contaminants from drinking water, but their performance for bacterial contamination is poor. Here, we develop a novel AER (AER6-1) with exceptional bactericidal effects and ultrafast adsorption rates of extracellular DNA (eDNA) (2.2- and 11.5-fold compared to other AERs) achieved through preloading quaternary ammonium groups (QAGs) with hexyl chain (-C6-N+-) on the resin exterior and successively grafting QAGs with a methyl chain (-C1-N+-) inside a resin pore. The AER6-1 outperforms other commercial AERs and ultraviolet disinfection, exhibiting superior elimination of total bacteria, potential pathogens (Escherichia coli and Pseudomonas aeruginosa), eDNA, and antibiotic resistance genes (mexF, mexB, and bacA) in actual drinking water, while maintaining a comparable anion exchange capacity with other commercial AERs. Theoretical calculations of density functional theory and xDLVO combined with XPS elucidate the crucial roles of hydrogen bonding and hydrophobic force provided by the resin skeleton and -C6-N+- in cleaving the bacterial cell membrane and increasing the adsorption kinetics on eDNA. This study broadens the scope of AERs and highlights an effective way of simultaneously removing bacterial and anionic contaminants from drinking water.

Phosphorylation-amplified synchronized droplet microfluidics sensitizes bacterial growth kinetic real-time monitoring

The necessity for rapid and accurate bacterial growth monitoring is imperative across various domains, including healthcare and environmental safety. We introduce the self-synchronized droplet-amplified electrical screening cytometry (SYNC) system, a novel meld of droplet microfluidics and electrochemical amplification tailored for precise bacterial growth kinetic monitoring. SYNC encapsulates single bacteria in picolitre droplets, enabling real-time, fluorescence-free electrochemical monitoring. A specially devised phosphorylation-amplified culture medium translates bacterial metabolic activity into discernible electrical impedance changes. The dual-channel design and a rail-based structure in SYNC facilitate parallel screening and self-synchronization of droplets, addressing the limitations of conventional impedance cytometry. SYNC showcases a 5-fold enhancement in detection sensitivity and reduces 50% of the detection time compared to traditional approaches. Notably, SYNC is pioneering in providing exact initial bacterial concentrations, achieve to 104 bacteria/ml, a capability unmatched by existing real-time techniques measuring electrochemical variations. Along with its robust performance, this earmarks SYNC as a powerful tool for applications such as antibiotic susceptibility testing, food quality monitoring, and real-time water bacteria monitoring, paving the way for enhanced microbial process management and infection control.

Microbial drinking water monitoring now and in the future

Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.

Nanowire-assisted electroporation via inducing cell destruction for inhibiting formation of VBNC bacteria: Comparison with chlorination

The induction of viable but nonculturable (VBNC) bacteria with cellular integrity and low metabolic activity by chemical disinfection causes a significant underestimation of potential microbiological risks in drinking water. Herein, a physical Co3O4 nanowire-assisted electroporation (NW-EP) was developed to induce cell damage via the locally enhanced electric field over nanowire tips, potentially achieving effective inhibition of VBNC cells as compared with chemical chlorination (Cl2). NW-EP enabled over 5-log removal of culturable cell for various G+/G- bacteria under voltage of 1.0 V and hydraulic retention time of 180 s, and with ∼3-6 times lower energy consumption than Cl2. NW-EP also achieved much higher removals (∼84.6 % and 89.5 %) of viable Bacillus cereus (G+) and Acinetobacter schindleri (G-) via generating unrecoverable pores on cell wall and reversible/irreversible pores on cell membrane than Cl2 (∼28.6 % and 41.1 %) with insignificant cell damage. The residual VBNC bacteria with cell wall damage and membrane pore resealing exhibited gradual inactivation by osmotic stress, leading to ∼99.8 % cell inactivation after 24 h storage (∼59.4 % for Cl2). Characterizations of cell membrane integrity and cell morphology revealed that osmotic stress promoted cell membrane damage for the gradual inactivation of VBNC cells during storage. The excellent adaptability of NW-EP for controlling VBNC cells in DI, tap and lake waters suggested its promising application potentials for drinking water, such as design of an external device on household taps.

Investigating the suitability of online flow cytometry for monitoring full-scale drinking water ozone system disinfection effectiveness

While online monitoring of physicochemical parameters has widely been incorporated into drinking water treatment systems, online microbial monitoring has lagged behind, resulting in the use of surrogate parameters (disinfectant residual, applied dose, concentration × time, CT) to assess disinfection system performance. Online flow cytometry (online FCM) allows for automated quantification of total and intact microbial cells. This study sought to investigate the feasibility of online FCM for full-scale drinking water ozone disinfection system performance monitoring. A water treatment plant with high lime solids turbidity in the ozone contactor influent was selected to evaluate the online FCM in challenging conditions. Total and intact cell counts were monitored for 40 days and compared to surrogate parameters (ozone residual, ozone dose, and CT) and grab sample assay results for cellular adenosine triphosphate (cATP), heterotrophic plate counts (HPC), impedance flow cytometry, and 16S rRNA gene sequencing. Online FCM provided insight into the dynamics of the full-scale ozone system, including offering early warning of increased contactor effluent cell concentrations, which was not observed using surrogate measures. Positive correlations were observed between online FCM intact cell counts and cATP levels (Kendall's tau=0.40), HPC (Kendall's tau=0.20), and impedance flow cytometry results (Kendall's tau=0.30). Though a strong correlation between log intact cell removal and CT was not observed, 16S rRNA gene sequencing results showed that passage through the ozone contactor significantly changed the microbial community (p < 0.05). Potential causes of the low overall cell inactivation in the contactor and the significant changes in the microbial community after ozonation include regrowth in the later chambers of the contactor and varied ozone resistance of drinking water microorganisms. This study demonstrates the suitability of direct, online microbial analysis for monitoring full-scale disinfection systems.

Enhancing the DNA yield intended for microbial sequencing from a low-biomass chlorinated drinking water

DNA extraction yield from drinking water distribution systems and premise plumbing is a key metric for any downstream analysis such as 16S amplicon or metagenomics sequencing. This research aimed to optimize DNA yield from low-biomass (chlorinated) reverse osmosis-produced tap water by evaluating the impact of different factors during the DNA extraction procedure. The factors examined are (1) the impact of membrane materials and their pore sizes; (2) the impact of different cell densities; and (3) an alternative method for enhancing DNA yield via incubation (no nutrient spiking). DNA from a one-liter sampling volume of RO tap water with varying bacterial cell densities was extracted with five different filter membranes (mixed ester cellulose 0.2 μm, polycarbonate 0.2 μm, polyethersulfone 0.2 and 0.1 μm, polyvinylidene fluoride 0.1 μm) for biomass filtration. Our results show that (i) smaller membrane pore size solely did not increase the DNA yield of low-biomass RO tap water; (ii) the DNA yield was proportional to the cell density and substantially dependent on the filter membrane properties (i.e., the membrane materials and their pore sizes); (iii) by using our optimized DNA extraction protocol, we found that polycarbonate filter membrane with 0.2 μm pore size markedly outperformed in terms of quantity (DNA yield) and quality (background level of 16S gene copy number) of recovered microbial DNA; and finally, (iv) for one-liter sampling volume, incubation strategy enhanced the DNA yield and enabled accurate identification of the core members (i.e., Porphyrobacter and Blastomonas as the most abundant indicator taxa) of the bacterial community in low-biomass RO tap water. Importantly, incorporating multiple controls is crucial to distinguish between contaminant/artefactual and true taxa in amplicon sequencing studies of low-biomass RO tap water.

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.

An Indirect Fluorescence Microscopy Method to Assess Vaginal Lactobacillus Concentrations

Lactobacillus species are the main colonizers of the vaginal microbiota in healthy women. Their absolute quantification by culture-based methods is limited due to their fastidious growth. Flow cytometry can quantify the bacterial concentration of these bacteria but requires the acquisition of expensive equipment. More affordable non-culturable methods, such as fluorescence microscopy, are hampered by the small size of the bacteria. Herein, we developed an indirect fluorescence microscopy method to determine vaginal lactobacilli concentration by determining the correlation between surface area bacterial measurement and initial concentration of an easily cultivable bacterium (Escherichia coli) and applying it to lactobacilli fluorescence microscopy counts. In addition, vaginal lactobacilli were quantified by colony-forming units and flow cytometry in order to compare these results with the indirect method results. The colony-forming-unit values were lower than the results obtained from the other two techniques, while flow cytometry and fluorescence microscopy results agreed. Thus, our developed method was able to accurately quantify vaginal lactobacilli.

Ensuring microbial water quality for on-site water reuse: Importance of online sensors for reliable operation

A growing number of cities and regions are promoting or mandating on-site treatment and reuse of wastewater, which has resulted in the implementation of several thousand on-site water reuse systems on a global scale. However, there is only limited information on the (microbial) water quality from implemented systems. The focus of this study was on two best-in-class on-site water reuse systems in Bengaluru, India, which typically met the local water quality requirements during monthly compliance testing. This study aimed to (i) assess the microbial quality of the reclaimed water at a high temporal resolution (daily or every 15 min), and (ii) explore whether measurements from commercially available sensors can be used to improve the operation of such systems. The monitoring campaign revealed high variations in microbial water quality, even in these best-in-class systems, rendering the water inadequate for the intended reuse applications (toilet flushing and landscape irrigation). These variations were attributed to two key factors: (1) the low frequency of chlorination, and (2) fluctuations of the chlorine demand of the water, in particular of ammonium concentrations. Such fluctuations are likely inherent to on-site systems, which rely on a low level of process control. The monitoring campaign showed that the microbial water quality was most closely related to oxidation-reduction potential (ORP) and free chlorine sensors. Due to its relatively low cost and low need for maintenance, the ORP emerges as a compelling candidate for automating the chlorination to effectively manage variations in chlorine demand and ensure safe water reuse. Overall, this study underscores the necessity of integrating treatment trains, operation, and monitoring for safe on-site water reuse.

Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques

Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.

Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes

Quantification of the abundance and understanding of the dynamics of the microbial communities is essential to establish a basis for microbiome characterization. The conventional techniques used for the quantification of microbes are complicated and time-consuming. With scientific advancement, many techniques evolved and came into account. Among them, flow cytometry is a robust, high-throughput technique through which microbial dynamics, morphology, microbial distribution, physiological characteristics, and many more attributes can be studied in a high-throughput manner with comparatively less time and resources. Flow cytometry, when combined with other omics-based methods, offers a rapid and efficient platform to analyze and understand the composition of microbiome at the cellular level. The microbial diversity observed through flow cytometry will not be equivalent to that obtained by sequencing methods, but this integrated approach holds great potential for high throughput characterization of microbiomes. Flow cytometry is regarded as an established characterization tool in haematology, oncology, immunology, and medical microbiology research; however, its application in environmental microbiology is yet to be explored. This comprehensive review aims to delve into the diverse environmental applications of flow cytometry across various domains, including but not limited to bioremediation, landfills, anaerobic digestion, industrial bioprocesses, water quality regulation, and soil quality regulation. By conducting an in-depth analysis, this article seeks to shed light on the potential benefits and challenges associated with the utilization of flow cytometry in addressing environmental concerns.

Self-repair and resuscitation of viable injured bacteria in chlorinated drinking water: Achromobacter as an example

Chlorine disinfection for the treatment of drinking water can cause injury to the membrane and DNA of bacterial cells and may induce the surviving injured bacteria into a viable but non-culturable (VBNC) state. It is difficult to monitor viable injured bacteria by heterotrophic plate counting (HPC), and their presence is also easily miscalculated in flow cytometry intact cell counting (FCM-ICC). Viable injured bacteria have a potential risk of resuscitation in drinking water distribution systems (DWDSs) and pose a threat to public health when drinking from faucets. In this study, bacteria with injured membranes were isolated from chlorinated drinking water by FCM cell sorting. The culture rate of injured bacteria varied from 0.08% to 2.6% on agar plates and 0.39% to 6.5% in 96-well plates. As the dominant genus among the five identified genera, as well as an opportunistic pathogen with multiple antibiotic resistance, Achromobacter was selected and further studied. After treatment with chlorine at a concentration of 1.2 mg/L, Achromobacter entered into the intermediate injured state on the FCM plot, and the injury on the bacterial surface was observed by electron microscopy. However, the CTC respiratory activity assay showed that 75.0% of the bacteria were still physiologically active, and they entered into a VBNC state. The injured VBNC Achromobacter in sterile drinking water were resuscitated after approximately 25 h. The cellular repair behavior of injured bacteria was studied by Fourier transform infrared attenuated total reflectance (FTIR-ATR) and comet assays. It was found that DNA injury rather than membrane injury was repaired first. The expression of Ku and ligD increased significantly during the DNA repair period, indicating that non-homologous end-joining (NHEJ) played an important role in repairing DNA double-strand breaks. This study deepened the understanding of the effect of chlorine disinfection on bacterial viability in drinking water and will provide support for the improvement of the chlorine disinfection process for the treatment of drinking water.

A downstream process control tool based on the redox dye resazurin for rapid and accurate measurement of microbial metabolic activity

Many sophisticated water treatment plants need a reliable, fast, and economical microbial load detection method. We refined a colorimetric assay using the redox dye resazurin to assess viable microorganisms. Here, we have used a mixed bacterial suspension of significant multi-drug-resistant coliform bacteria isolated from hospital wastewater and constructed a resazurin reduction calibration curve which could accurately predict the level of microbial contamination. The number of viable microorganisms was calculated from calibration curve in terms of log colony forming units (CFU) per milliliter. Ultrasonication disinfection of bacterial suspension for a duration of 50 min measured by resazurin assay depicted a reduction of 16.94%, 26.48%, and 37.69% at 410 W, 580 W, and 700 W, respectively. A synergistic effect of the combined methods of ultrasonication and heat disinfection treatments on raw wastewater and secondary wastewater effluent was observed and was also evaluated using both resazurin assay and standard plate count method. For raw wastewater, about 1.8 log reduction was observed for ultrasonication alone and 4 log CFU/mL reduction for thermosonication. In the secondary wastewater effluent, a reduction of 2.9 and 3.2 log CFU/mL was recorded for ultrasonication and thermosonication respectively. Resazurin microbial viability test results were highly comparable with conventional colony plate count for all treatment procedures, suggesting its appropriateness for quick and reliable wastewater sample microbial viability monitoring.

Opportunities in optical and electrical single-cell technologies to study microbial ecosystems

New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.

Predicting heterotrophic plate count exceedance in tap water: A binary classification model supervised by culture-independent data

Culture-independent data can be utilized to identify heterotrophic plate count (HPC) exceedances in drinking water. Although HPC represents less than 1% of the bacterial community and exhibits time lags of several days, HPC data are widely used to assess the microbiological quality of drinking water and are incorporated into drinking water standards. The present study confirmed the nonlinear relationships between HPC, intact cell count (ICC), and adenosine triphosphate (ATP) in tap water samples (stagnant and flushed). By using a combination of ICC, ATP, and free chlorine data as inputs, we show that HPC exceedance can be classified using a 2-layer feed-forward artificial neural network (ANN). Despite the nonlinearity of HPC, the best binary classification model showed accuracies of 95%, sensitivity of 91%, and specificity of 96%. ICC and chlorine concentrations were the most important features for classifiers. The main limitations, such as sample size and class imbalance, were also discussed. The present model provides the ability to convert data from emerging measurement techniques into established and well-understood measures, overcoming culture dependence and offering near real-time data to help ensure the biostability and safety of drinking water.

Development of an Automated Online Flow Cytometry Method to Quantify Cell Density and Fingerprint Bacterial Communities

Cell density is an important factor in all microbiome research, where interactions are of interest. It is also the most important parameter for the operation and control of most biotechnological processes. In the past, cell density determination was often performed offline and manually, resulting in a delay between sampling and immediate data processing, preventing quick action. While there are now some online methods for rapid and automated cell density determination, they are unable to distinguish between the different cell types in bacterial communities. To address this gap, an online automated flow cytometry procedure is proposed for real-time high-resolution analysis of bacterial communities. On the one hand, it allows for the online automated calculation of cell concentrations and, on the other, for the differentiation between different cell subsets of a bacterial community. To achieve this, the OC-300 automation device (onCyt Microbiology, Zürich, Switzerland) was coupled with the flow cytometer CytoFLEX (Beckman Coulter, Brea, USA). The OC-300 performs the automatic sampling, dilution, fixation and 4',6-diamidino-2-phenylindole (DAPI) staining of a bacterial sample before sending it to the CytoFLEX for measurement. It is demonstrated that this method can reproducibly measure both cell density and fingerprint-like patterns of bacterial communities, generating suitable data for powerful automated data analysis and interpretation pipelines. In particular, the automated, high-resolution partitioning of clustered data into cell subsets opens up the possibility of correlation analysis to identify the operational or abiotic/biotic causes of community disturbances or state changes, which can influence the interaction potential of organisms in microbiomes or even affect the performance of individual organisms.

Predicting microbial water quality in on-site water reuse systems with online sensors

Widespread implementation of on-site water reuse is hindered by the limited availability of monitoring approaches that ensure microbial quality during operation. In this study, we developed a methodology for monitoring microbial water quality in on-site water reuse systems using inexpensive and commercially available online sensors. An extensive dataset containing sensor and microbial water quality data for six of the most critical types of disruptions in membrane bioreactors with chlorination was collected. We then tested the ability of three typological machine learning algorithms - logistic regression, support-vector machine, and random forest - to predict the microbial water quality as "safe" or "unsafe" for reuse. The main criteria for model optimization was to ensure a low false positive rate (FPR) - the percentage of safe predictions when the actual condition is unsafe - which is essential to protect users health. This resulted in enforcing a fixed FPR ≤ 2%. Maximizing the true positive rate (TPR) - the percentage of safe predictions when the actual condition is safe - was given second priority. Our results show that logistic-regression-based models using only two out of the six sensors (free chlorine and oxidation-reduction potential) achieved the highest TPR. Including sensor slopes as engineered features allowed to reach similar TPRs using only one sensor instead of two. Analysis of the occurrence of false predictions showed that these were mostly early alarms, a characteristic that could be regarded as an asset in alarm management. In conclusion, the simplest algorithm in combination with only one or two sensors performed best at predicting the microbial water quality. This result provides useful insights for water quality modeling or for applications where small datasets are a common challenge and a general advantage might be gained by using simpler models that reduce the risk of overfitting, allow better interpretability, and require less computational power.

Dry alginate beads for fecal microbiota transplantation: from model strains to fecal samples

Clostridioides difficile infection (CDI) is a critical nosocomial infection with more than 124,000 cases per year in Europe and a mortality rate of 15-17%. The standard of care (SoC) is antibiotic treatment. Unfortunately, the relapse rate is high (∼35%) and SoC is significantly less effective against recurrent infection (rCDI). Fecal microbiota transplantation (FMT) is a recommended treatment against rCDI from the second recurrence episode and has an efficacy of 90%. The formulation of diluted donor stool deserves innovation because its actual administration routes deserve optimization (naso-duodenal/jejunal tubes, colonoscopy, enema or several voluminous oral capsules). Encapsulation of model bacteria strains in gel beads were first investigated. Then, the encapsulation method was applied to diluted stools. Robust spherical gel beads were obtained. The mean particle size was around 2 mm. A high loading of viable microorganisms was obtained for model strains and fecal samples. For plate-counting, values ranged from 10¹⁵ to 10¹⁷ CFU/g for single and mixed model strains, and 10⁶ to 10⁸ CFU/g for fecal samples. This corresponded to a viability of 30% to 60% as assessed by flow cytometry. This novel formulation is promising as the technology is applicable to both model strains and bacteria contained in the gut microbiota.

Molecular testing devices for on-site detection of E. coli in water samples

Escherichia coli (E. coli) cells are present in fecal materials that can be the main source for disease-causing agents in water. As a result, E. coli is recommended as a water quality indicator. We have developed an innovative platform to detect E. coli for monitoring water quality on-site by integrating paper-based sample preparation with nucleic acid isothermal amplification. The platform carries out bacterial lysis and DNA enrichment onto a paper pad through ball-based valves for fluid control, with no need of laboratory equipment, followed by loop-mediated isothermal amplification (LAMP) in a battery-operated coffee mug, and colorimetric detection. We have used the platform to detect E. coli in environmental water samples in about 1 h, with a limit of quantitation of 0.2 CFU/mL, and 3 copies per reaction. The platform was confirmed for detecting multiple E. coli strains, and for water samples of different salt concentrations. We validated the functions of the platform by analyzing recreational water samples collected near the Atlantic Ocean that contain different concentrations of salt and bacteria.

Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic

COVID-19 pandemic-related building restrictions heightened drinking water microbiological safety concerns post-reopening due to the unprecedented nature of commercial building closures. Starting with phased reopening (i.e., June 2020), we sampled drinking water for 6 months from three commercial buildings with reduced water usage and four occupied residential households. Samples were analyzed using flow cytometry and full-length 16S rRNA gene sequencing along with comprehensive water chemistry characterization. Prolonged building closures resulted in 10-fold higher microbial cell counts in the commercial buildings [(2.95 ± 3.67) × 105 cells mL-1] than in residential households [(1.11 ± 0.58) × 104 cells mL-1] with majority intact cells. While flushing reduced cell counts and increased disinfection residuals, microbial communities in commercial buildings remained distinct from those in residential households on the basis of flow cytometric fingerprinting [Bray-Curtis dissimilarity (dBC) = 0.33 ± 0.07] and 16S rRNA gene sequencing (dBC = 0.72 ± 0.20). An increase in water demand post-reopening resulted in gradual convergence in microbial communities in water samples collected from commercial buildings and residential households. Overall, we find that the gradual recovery of water demand played a key role in the recovery of building plumbing-associated microbial communities as compared to short-term flushing after extended periods of reduced water demand.

Occurrence and control of fungi in water: New challenges in biological risk and safety assurance

Recently, the contamination of fungi in water has aroused widespread concern, which will pose a threat to water quality and safety, and raise diseases risk in the immunocompromised individuals. In this review, the characteristics and different physiological state of fungi in water are summarized. A comprehensive evaluation of the control efficiency and mechanism of waterborne fungi by the commonly used disinfection methods is provided as well. During the disinfection processes of chlorine, chlorine dioxide, chloramine and advanced disinfection processes (ADPs) such as O₃-based ADPs and UV-based ADPs, the fungal spores firstly lost their culturability, followed by membrane integrity, and the intracellular reactive oxygen species level increased at the same time, eventually the fungal spores were completely inactivated. The security strategies of drinking water against the contamination of fungi are also discussed in terms of water sources, water treatment plants and pipe network. Finally, future researches need to be explored are proposed: the rapid detection methods, the production laws and control of mycotoxin, and the outbreak conditions of fungi in water. Specifically, exploring efficient, safe and economical technologies, especially ADPs, is still the main direction in the disinfection of fungi in future studies. This review can offer a comprehensive understanding on the occurrence and control of fungi in water to fill the knowledge gap and provide guidance for the future research.

Sensor setpoints that ensure compliance with microbial water quality targets for membrane bioreactor and chlorination treatment in on-site water reuse systems

Widespread implementation of on-site water reuse systems is hindered by the limited ability to ensure the level of treatment and protection of human health during operation. In this study, we tested the ability of five commercially available online sensors (free chlorine (FC), oxidation-reduction potential (ORP), pH, turbidity, UV absorbance at 254 nm) to predict the microbial water quality in membrane bioreactors followed by chlorination using logistic regression-based and mechanism-based models. The microbial water quality was assessed in terms of removal of enteric bacteria from the wastewater, removal of enteric viruses, and regrowth of bacteria in the treated water. We found that FC and ORP alone could predict the microbial water quality well, with ORP-based models generally performing better. We further observed that prediction accuracy did not increase when data from multiple sensors were integrated. We propose a methodology to link online sensor measurements to risk-based water quality targets, providing operation setpoints protective of human health for specific combinations of wastewaters and reuse applications. For instance, we recommend a minimum ORP of 705 mV to ensure a virus log-removal of 5, and an ORP of 765 mV for a log-removal of 6. These setpoints were selected to ensure that the percentage of events where the water is predicted to meet the quality target but it does not remains below 5%. Such a systematic approach to set sensor setpoints could be used in the development of water reuse guidelines and regulations that aim to cover a range of reuse applications with differential risks to human health.

Microbial Water Quality through a Full-Scale Advanced Wastewater Treatment Demonstration Facility

The fates of viruses, bacteria, and antibiotic resistance genes during advanced wastewater treatment are important to assess for implementation of potable reuse systems. Here, a full-scale advanced wastewater treatment demonstration facility (ozone, biological activated carbon filtration, micro/ultrafiltration, reverse osmosis, and advanced oxidation) was sampled over three months. Atypically, no disinfectant residual was applied before the microfiltration step. Microbial cell concentrations and viability were assessed via flow cytometry and adenosine triphosphate (ATP). Concentrations of bacteria (16S rRNA gene), viruses (human adenovirus and JC polyomavirus), and antibiotic resistance genes (sul1 and bla _TEM ) were assessed via quantitative PCR following the concentration of large sample volumes by dead-end ultrafiltration. In all membrane filtration permeates, microbial concentrations were higher than previously reported for chloraminated membranes, and log₁₀ reduction values were lower than expected. Concentrations of 16S rRNA and sul1 genes were reduced by treatment but remained quantifiable in reverse osmosis permeate. It is unclear whether sul1 in the RO permeate was from the passage of resistance genes or new growth of microorganisms, but the concentrations were on the low end of those reported for conventional drinking water distribution systems. Adenovirus, JC polyomavirus, and bla _TEM genes were reduced below the limit of detection (∼10^-2 gene copies per mL) by microfiltration. The results provide insights into how treatment train design and operation choices affect microbial water quality as well as the use of flow cytometry and ATP for online monitoring and process control.

Shower water contributes viable nontuberculous mycobacteria to indoor air

Nontuberculous mycobacteria (NTM) are frequently present in municipal drinking water and building plumbing, and some are believed to cause respiratory tract infections through inhalation of NTM-containing aerosols generated during showering. However, the present understanding of NTM transfer from water to air is insufficient to develop NTM risk mitigation strategies. This study aimed to characterize the contribution of shower water to the abundance of viable NTM in indoor air. Shower water and indoor air samples were collected, and 16S rRNA and rpoB genes were sequenced. The sequencing results showed that running the shower impacted the bacterial community structure and NTM species composition in indoor air by transferring certain bacteria from water to air. A mass balance model combined with NTM quantification results revealed that on average 1/132 and 1/254 of NTM cells in water were transferred to air during 1 hour of showering using a rain and massage showerhead, respectively. A large fraction of the bacteria transferred from water to air were membrane-damaged, i.e. they had compromised membranes based on analysis by live/dead staining and flow cytometry. However, the damaged NTM in air were recoverable as shown by growth in a culture medium mimicking the respiratory secretions of people with cystic fibrosis, implying a potential infection risk by NTM introduced to indoor air during shower running. Among the recovered NTM, Mycobacterium mucogenicum was the dominant species as determined by rpoB gene sequencing. Overall, this study lays the groundwork for future pathogen risk management and public health protection in the built environment.

Scientific concepts and methods for moving persistence assessments into the 21st century

The evaluation of a chemical substance's persistence is key to understanding its environmental fate, exposure concentration, and, ultimately, environmental risk. Traditional biodegradation test methods were developed many years ago for soluble, nonvolatile, single-constituent test substances, which do not represent the wide range of manufactured chemical substances. In addition, the Organisation for Economic Co-operation and Development (OECD) screening and simulation test methods do not fully reflect the environmental conditions into which substances are released and, therefore, estimates of chemical degradation half-lives can be very uncertain and may misrepresent real environmental processes. In this paper, we address the challenges and limitations facing current test methods and the scientific advances that are helping to both understand and provide solutions to them. Some of these advancements include the following: (1) robust methods that provide a deeper understanding of microbial composition, diversity, and abundance to ensure consistency and/or interpret variability between tests; (2) benchmarking tools and reference substances that aid in persistence evaluations through comparison against substances with well-quantified degradation profiles; (3) analytical methods that allow quantification for parent and metabolites at environmentally relevant concentrations, and inform on test substance bioavailability, biochemical pathways, rates of primary versus overall degradation, and rates of metabolite formation and decay; (4) modeling tools that predict the likelihood of microbial biotransformation, as well as biochemical pathways; and (5) modeling approaches that allow for derivation of more generally applicable biotransformation rate constants, by accounting for physical and/or chemical processes and test system design when evaluating test data. We also identify that, while such advancements could improve the certainty and accuracy of persistence assessments, the mechanisms and processes by which they are translated into regulatory practice and development of new OECD test guidelines need improving and accelerating. Where uncertainty remains, holistic weight of evidence approaches may be required to accurately assess the persistence of chemicals. Integr Environ Assess Manag 2022;18:1454-1487. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Investigation of the effect of sustainable magnetic treatment on the microbiological communities in drinking water

The drinking water scarcity is posing a threat to mankind, hence better water quality management methods are required. Magnetic water treatment, which has been reported to improve aesthetic water quality and reduce scaling problems, can be an important addition to the traditional disinfectant dependent treatment. Despite the extensive market application opportunities, the effect of magnetic fields on (microbial) drinking water communities and subsequently the biostability is still largely unexplored, although the first patent was registered already 1945. Here flow cytometry was applied to assess the effect of weak magnetic fields (≤10 G) with strong gradients (≈800 G/m) on drinking water microbial communities. Drinking water was collected from the tap and placed inside the magnetic field (treated) and 5 m away from the magnet to avoid any background interferences (control) using both a static set-up and a shaking set-up. Samples were collected during a seven-day period for flow cytometry examination. Additionally, the effects of magnetic fields on the growth of Pseudomonas aeruginosa in autoclaved tap water were examined. Based on the fluorescent intensity of the stained nucleic acid content, the microbial cells were grouped into low nucleic acid content (LNA) and high nucleic acid content (HNA). Our results show that the LNA was dominant under nutrient limited condition while the HNA dominates when nutrient is more available. Such behavior of LNA and HNA matches well with the long discussed r/K selection model where r-strategists adapted to eutrophic conditions and K-strategists adapted to oligotrophic conditions. The applied magnetic fields selectively promote the growth of LNA under nutrient rich environment, which indicates a beneficial effect on biostability enhancement. Inhibition on an HNA representative Pseudomonas aeruginosa has also been observed. Based on our laboratory observations, we conclude that magnetic field treatment can be a sustainable method for microbial community management with great potential.

Measuring Single Bacterial Viability in Optical Traps with a Power Sweeping Technique

Assessing bacterial viability is crucial in public health, food safety, environmental microbiology, and other relevant fields. The classical agar plate counting method and the popular dye-based assays have shown their strengths, but they also have limitations including high time consumption, relatively complex sample preparations, and cytotoxicity. In this work, we present a new bacterial viability assay based on optical tweezers utilizing a power sweeping strategy. By monitoring and analyzing bacterial nanomotion in optical traps under different trapping laser powers, the slope of the proportionality between the quantified extent of motion and the trapping laser power was defined as the mobility restriction coefficient (MRC) to quantify bacterial viability. We first established a firm correlation between the viability and MRC by measuring alive and dead Escherichia coli and Photobacterium phosphoreum. Then the capability of real-time long-term characterization of the assay was validated by measuring the viability of individual P. phosphoreum while regulating the viability with an inactivation light. Notably, a 'spinning-induced stabilization' mechanism was proposed to explain the surprising increase of apparent bacterial mobility after inactivation. Overall, the assay was proved to be a reliable label-free bacterial viability assay at a single-cell level, which holds potential in antibiotic susceptibility testing, drug screening, and rapid diagnostics.

Flow cytometric assessment of the chlorine/chloramine efficacy of particle-associated bacteria in drinking water

Chlorine and chloramine are widely used to maintain the microbial safety after drinking water treatment plants. Particles existing in the treated water may react with these chemical disinfectants, and impact the efficacy of disinfection. However, the protective effects of particles without-disinfectant demand on bacteria in the chlorination/chloramination are not well known. In this study, two laboratory-derived bacteria (Staphylococcus aureus and Escherichia coli) and two no-disinfectant demand particles (Fe₂O₃ and kaolin) in drinking water were selected to build particle-associated bacteria (PAB) systems, and their resistance to chlorine/chloramine was further assessed. Flow cytometry (FCM) was employed to image PAB systems and assess the removal rate of bacteria. The results were that particles showed protective effects on bacteria in half of chlorine experiments and 90% of chloramination. The protection was related to the combination form of particles and bacteria tied to neither particle species nor size, and there was no positive relationship between the protection effect and water turbidity. S. aureus attached to Fe₂O₃ had stronger resistance than kaolin, and kaolin protected E. coli better than Fe₂O₃. The same trend was observed in both chemical disinfectants, and more significant resistance had been shown in chloramination than chlorination. FCM images which gave a qualitative description on the combination states of different PAB systems may be a clue to explain the strength of the resistance. Environmental bacterial strains and particles are recommended in the future to explore practical applications.

Fungal-sponge composite carriers coupled with denitrification and biomineralization bacteria to remove nitrate, calcium, and cadmium in a bioreactor

The coexistence of nitrate (NO₃^--N) and heavy metals in the aquatic environment causes harm to both the aquatic ecosystem and human health. Here, fungal-sponge composite carriers (FSC) were assembled and immobilized with strain WZ39 in a bioreactor to remove NO₃^--N, Ca²⁺, and Cd²⁺. Stable bioreactor performance under heavy metal pressure was achieved. The highest removal efficiencies of NO₃^--N, Ca²⁺, and Cd²⁺ reached 100, 71.81, and 92.50%, respectively. Bacteria and precipitates were found in fungal mycelium and sponge. The precipitates composed of Ca_3.9(Ca_4.7Cd_0.7)(PO₄)₆(OH)_1.8, CaCO₃, and CdCO₃. Fluorescence excitation-emission matrix (EEM) and flow cytometric (FCM) analysis indicated bacteria in FSC exhibited a strong metabolic activity and high percentage of intact cells under heavy metal stress. High-throughput sequencing results showed Pseudomonas sp. WZ39 played a major role in the bioreactor. The potential functions associated with metabolism, heavy metal transfer, and biofilm formation had high relative abundance in the bioreactor.

Exploring the use of flow cytometry for understanding the efficacy of disinfection in chlorine contact tanks

A pilot scale chlorine contact tank (CCT) with flexible baffling was installed at an operational water treatment plant (WTP), taking a direct feed from the outlet of the rapid gravity filters (RGF). For the first time, disinfection efficacy was established by direct microbial monitoring in a continuous reactor using flow cytometry (FCM). Disinfection variables of dose, time, and hydraulic efficiency (short circuiting and dispersion) were explored following characterisation of the reactor's residence time distributions (RTD) by tracer testing. FCM enabled distinction to be made between changes in disinfection reactor design where standard culture-based methods could not. The product of chlorine concentration (C) and residence time (t) correlated well with inactivation of microbes, organisms, with the highest cell reductions (N/N₀) reaching <0.025 at Ct_x¯ of 20 mg.min/L and above. The influence of reactor geometry on disinfection was best shown from the Ct₁₀. This identified that the initial level of microbial inactivation was higher in unbaffled reactors for low Ct₁₀ values, although the highest levels of inactivation of 0.015 could only be achieved in the baffled reactors, because these conditions enabled the highest Ct₁₀ values to be achieved. Increased levels of disinfection were closely associated with increased formation of the trihalomethane disinfection by-products. The results highlight the importance of well-designed and operated CCT. The improved resolution afforded by FCM provides a tool that can dynamically quantify disinfection processes, enabling options for much better process control.

Real-Time Monitoring of Dynamic Microbial Fe(III) Respiration Metabolism with a Living Cell-Compatible Electron-Sensing Probe

Monitoring microbial metabolism is vital for biomanufacturing processes optimization. However, it remains a grand challenge to offer insight into microbial metabolism due to particularly complex and dynamic processes. Here, we report an electron-sensing probe Zn₂ GeO₄ :Mn@Fe³⁺ for real-time and dynamic monitoring of Fe(III) respiration metabolism. The quenched persistent luminescence of Zn₂ GeO4:Mn@Fe³⁺ is recovered when Fe³⁺ accepted electrons from the dynamic Fe(III) respiration metabolism, enabling the real-time monitoring of microbial metabolism. The probe shows the capability to verify the role of related biomolecules in microbial Fe(III) respiration metabolism, to track the dynamic Fe(III) respiration metabolic response to environmental stress and microbial co-culture interactions. Furthermore, the Zn₂ GeO₄ :Mn@Fe³⁺ probe provides guidance for improving biosynthesis efficiency by monitoring Fe redox recycling in microbial co-culture.

Rapid Detection of Gram-Positive and -Negative Bacteria in Water Samples Using Mannan-Binding Lectin-Based Visual Biosensor

Waterborne bacterial infection is a health threat worldwide, making accurate and timely bacteria detection crucial to prevent waterborne disease outbreaks. Inspired by the intrinsic capability of mannan-binding lectin (MBL) in recognizing the pathogen-associated molecular patterns (PAMPs), a visual biosensor is developed here for the on-site detection of both Gram-positive and -negative bacteria. The biosensor was synthesized by immobilization of the MBL protein onto the blue carboxyl-functionalized polystyrene microparticles (PSM), which is then used in a two-step assay to detect bacterial cells in water samples. The first step involved a 20 min incubation following the MBL-PSM and calcium chloride solution addition to the samples. The second step was to add ethanol to the resultant blue mixture and observe the color change with the naked eye after 15 min. The biosensor had a binary (all-or-none) response, which in the presence of bacterial cells kept its blue color, while in their absence the color changed from blue to colorless. Testing the water samples spiked with four Gram-negative bacteria including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa and two Gram-positive bacteria of Enterococcus faecalis and Staphylococcus aureus showed that the biosensor could detect all tested bacteria with a concentration as low as 10^1.5 CFU/ml. The performance of biosensor using the water samples from a water treatment plant also confirmed its capability to detect the pathogens in real-life water samples without the need for instrumentation.

Online evaluation of bacterial cells in sand filter effluents during full-scale treatment of drinking water

Ensuring the microbiological safety of drinking water is critical to protect public health. This study aimed to evaluate the reliability of real-time bacteriological counter coupled with an online dialysis membrane-based pre-treatment system for continuously monitoring bacterial cell counts in sand filter effluents of a full-scale drinking water treatment plant. The pre-treatment system, which included anion exchange resins (porous polymeric microbeads that trap ions for releasing other ions) for dialysate regeneration, successfully achieved the stable attenuation of background interfering substances (humic acids) during the 19-d test. The real-time bacteriological counter equipped with the pre-treatment system provided a continuous profile of bacterial cell counts in the sand filter effluent (0.2-2.5 × 10⁴ counts/mL). The online analysis identified different timing of concentration peaks between particle and bacterial cell counts after backwashing. Bacterial community analysis revealed that Proteobacteria, Planctomycetes, and Cyanobacteria were the dominating phyla. Further, total bacterial cell counts determined by fluorescence microscopy and SYBR® Green I staining, a commonly accepted parameter, was found to be an indicator of online-monitored bacterial cell counts. The results indicated the potential of monitoring the bacterial cell counts in a sand filter process for providing an early warning of filter failures, which can allow plant operators to diagnose the overall system and provide countermeasures.

Seawater desalination based drinking water: Microbial characterization during distribution with and without residual chlorine

Monitoring the changes that occur to water during distribution is vital to ensure water safety. In this study, the biological stability of reverse osmosis (RO) produced drinking water, characterized by low cell concentration and low assimilable organic carbon, in combination with chlorine disinfection was investigated. Water quality at several locations throughout the existing distribution network was monitored to investigate whether microbial water quality changes can be identified. Results revealed that the water leaving the plant had an average bacterial cell concentration of 10³ cells/mL. A 0.5-1.5 log increase in bacterial cell concentration was observed at locations in the network. The residual disinfectant was largely dissipated in the network from 0.5 mg/L at the treatment plant to less than 0.1 mg/L in the network locations. The simulative study involving miniature distribution networks, mimicking the dynamics of a distribution network, fed with the RO produced chlorinated and non-chlorinated drinking water revealed that distributing RO produced water without residual disinfection, especially at high water temperatures (25-30 °C), poses a higher chance for water quality change. Within six months of operation of the miniature network fed with unchlorinated RO produced water, the adenosine triphosphate (ATP) and total cell concentration (TCC) in the pipe biofilm were 4 × 10² pg ATP/cm² and 1 × 10⁷ cells/ cm². The low bacterial cell concentration and organic carbon concentration in the RO-produced water did not prevent biofilm development inside the network with and without residual chlorine. The bacterial community analysis using 16S ribosomal RNA (rRNA) gene sequencing revealed that mesophilic bacteria with higher temperature tolerance and bacteria associated with oligotrophic, nutrient-poor conditions dominated the biofilm, with no indication of the existence of opportunistic pathogenic species. However, chlorination selected against most bacterial groups and the bacterial community that remained was mainly the bacteria capable of surviving disinfection regimes. Biofilms that developed in the presence of chlorine contained species classified as opportunistic pathogens. These biofilms have an impact on shaping the water quality received at the consumer tap. The presence of these bacteria on its own is not a health risk indicator; viability assessment and qPCRs targeting genes specific to the opportunistic pathogens as well as quantitative microbiological risk assessment (QMRA) should be included to assess the risk. The results from this study highlight the importance of implementing multiple barriers to ensure water safety. Changes in water quality detected even when high-quality disinfected RO-produced water is distributed highlight microbiological challenges that chlorinated systems endure, especially at high water temperatures.

An Integrative, Multiparametric Approach for the Comprehensive Assessment of Microbial Quality and Pollution in Aquaculture Systems

As the aquaculture sector significantly expanded worldwide in the past decades, the concept of sustainable aquaculture has developed with the challenge of not only maximizing benefits but also minimizing the negative impacts on the environment assuring, at the same time, food security. In this framework, monitoring and improving the microbiological water quality and animal health are a central topic. In the present study, we evaluated the seawater microbiological quality in a mariculture system located in a Mediterranean coastal area (Northern Ionian Sea, Italy). We furnished, for the first time, a microbial inventory based on conventional culture-based methods, integrated with the 16S rRNA gene metabarcoding approach for vibrios identification and diversity analyses, and further implemented with microbial metabolic profiling data obtained from the Biolog EcoPlate system. Microbiological pollution indicators, vibrios diversity, and microbial metabolism were determined in two different times of the year (July and December). All microbial parameters measured in July were markedly increased compared to those measured in December. The presence of potentially pathogenic vibrios is discussed concerning the risk of fish disease and human infections. Thus, the microbial inventory here proposed might represent a new multiparametric approach for the suitable surveillance of the microbial quality in a mariculture system. Consequently, it could be useful for ensuring the safety of both the reared species and the consumers in the light of sustainable, eco-friendly aquaculture management.

Automated flow cytometry as a flexible tool for comparing disinfection characteristics of indigenous bacterial communities and pure cultures

Bacterial inactivation efficiency of chlorine varies with organisms and environmental conditions. The comparability of different samples/studies, especially comparing indigenous bacterial communities with pure cultures, is impeded by inconsistent experimental conditions and analytical methods used in various studies. We tested a novel 96-well plate FCM experimental and automated analytical approach, where bacterial communities and pure cultures were suspended in the same natural water matrix prior to chlorination directly in the plate. We demonstrated the ability to rapidly monitor the efficiency of 32 different combinations of chlorine concentration and time (i.e. chlorine exposure) on bacterial pure cultures and indigenous aquatic communities, which enabled correct comparison of the data from different samples under the exact same experimental conditions. In this study, the 96-well plate automated FCM approach enabled large sets (896) of independent chlorination experiments to be carried out in a short time period. To our knowledge, this is the largest dataset of chlorination experiments which consumed least time (within 18 h after sampling) until now. Staining with SYBR Green I (SG) and SG combined with propidium iodide (SGPI) was used to assess cellular damage during chlorination. The results showed that with the same chlorine exposure, a higher chlorine concentration with a shorter contact time is favorable for inactivation of bacteria. Our research provides a promising framework to compare disinfection characteristics of various microorganism and can be further developed to diagnose effect of antimicrobial products.

Risks, characteristics, and control strategies of disinfection-residual-bacteria (DRB) from the perspective of microbial community structure

The epidemic of COVID-19 has aroused people's particular attention to biosafety. A growing number of disinfection products have been consumed during this period. However, the flaw of disinfection has not received enough attention, especially in water treatment processes. While cutting down the quantity of microorganisms, disinfection processes exert a considerable selection effect on bacteria and thus reshape the microbial community structure to a great extent, causing the problem of disinfection-residual-bacteria (DRB). These systematic and profound changes could lead to the shift in regrowth potential, bio fouling potential, as well as antibiotic resistance level and might cause a series of potential risks. In this review, we collected and summarized the data from the literature in recent 10 years about the microbial community structure shifting of natural water or wastewater in full-scale treatment plants caused by disinfection. Based on these data, typical DRB with the most reporting frequency after disinfection by chlorine-containing disinfectants, ozone disinfection, and ultraviolet disinfection were identified and summarized, which were the bacteria with a relative abundance of over 5% in the residual bacteria community and the bacteria with an increasing rate of relative abundance over 100% after disinfection. Furthermore, the phylogenic relationship and potential risks of these typical DRB were also analyzed. Twelve out of fifteen typical DRB genera contain pathogenic strains, and many were reported of great secretion ability. Pseudomonas and Acinetobacter possess multiple disinfection resistance and could be considered as model bacteria in future studies of disinfection. We also discussed the growth, secretion, and antibiotic resistance characteristics of DRB, as well as possible control strategies. The DRB phenomenon is not limited to water treatment but also exists in the air and solid disinfection processes, which need more attention and more profound research, especially in the period of COVID-19.

Comparing the bacterial growth potential of ultra-low nutrient drinking water assessed by growth tests based on flow cytometric intact cell count versus adenosine triphosphate

The bacterial growth potential (BGP) of drinking water is widely assessed either by flow cytometric intact cell count (BGP_ICC) or adenosine triphosphate (BGP_ATP) based methods. Combining BGP_ICC and BGP_ATP measurements has been previously applied for various types of drinking water having high to low growth potential. However, this has not been applied for water with ultra-low nutrient content, such as remineralised RO permeate. To conduct a sound comparison, conventionally treated drinking water was included in this study, which was also used as an inoculum source. BGP_ICC, BGP_ATP, intact cell-yield (Y_ICC), and ATP-yield (Y_ATP) were determined for conventionally treated drinking water (Tap-water) and remineralised RO permeate (RO-water). In addition, both BGP_ICC and BGP_ATP methods were used to identify the growth-limiting nutrient in each water type. The results showed that the BGP_ICC ratio between Tap-water/RO-water was ∼7.5, whereas the BGP_ATP ratio was only ∼4.5. Moreover, the Y_ICC ratio between Tap-water/RO-water was ∼2 (9.8 ± 0.6 × 10⁶ vs. 4.6 ± 0.8 × 10⁶ cells/µg-C), whereas the Y_ATP ratio was ∼1 (0.39 ± 0.12 vs. 0.42 ± 0.06 ng ATP/µg-C), resulting in a consistently higher ATP per cell in RO-water than that of Tap-water. Both BGP_ICC and BGP_ATP methods revealed that carbon was the growth-limiting nutrient in the two types of water. However, with the addition of extra carbon, phosphate limitation was detected only with the BGP_ICC method, whereas BGP_ATP was not affected, suggesting that a combination of carbon and phosphate is essential for biomass synthesis, whereas carbon is probably utilised for cellular activities other than cell synthesis when phosphate is limited. It was estimated that the intact cell-yield growing on phosphate would be 0.70 ± 0.05 × 10⁹ cells/µg PO₄-P.

An ultrasensitive fluorimetric sensor for pre-screening of water microbial contamination risk

In recent years, global efforts have been directed towards the development of water safety routines, consequently demanding cost-effective sensors capable of detecting outbreaks at early stages. This work reports the development and study of an original in-field tryptophan fluorimetric sensor as a potential indicator of real-time microbial contamination in water. The sensor excitation and emission wavelengths were selected with respect to the coliform bacteria tryptophan peak; 280 nm for excitation and 330 nm for emission. The in-lab tests with standard samples show a detection limit of 4.89 nM (≈0.1 μg/l) for L-tryptophan. The sensor exhibited good linearity over three orders of magnitude and considerable detection reproducibility, which was confirmed during calibration tests. Small-scale in situ tests showed that the sensor was better correlated with coliform bacteria than other online sensors such as turbidity. This suggests that the fluorimetric tryptophan sensor can be integrated into early warning systems that quickly assess changes in water microbial quality.

From Biogas and Hydrogen to Microbial Protein Through Co-Cultivation of Methane and Hydrogen Oxidizing Bacteria

Increasing efforts are directed towards the development of sustainable alternative protein sources among which microbial protein (MP) is one of the most promising. Especially when waste streams are used as substrates, the case for MP could become environmentally favorable. The risks of using organic waste streams for MP production-the presence of pathogens or toxicants-can be mitigated by their anaerobic digestion and subsequent aerobic assimilation of the (filter-sterilized) biogas. Even though methane and hydrogen oxidizing bacteria (MOB and HOB) have been intensively studied for MP production, the potential benefits of their co-cultivation remain elusive. Here, we isolated a diverse group of novel HOB (that were capable of autotrophic metabolism), and co-cultured them with a defined set of MOB, which could be grown on a mixture of biogas and H2/O2. The combination of MOB and HOB, apart from the CH4 and CO2 contained in biogas, can also enable the valorization of the CO2 that results from the oxidation of methane by the MOB. Different MOB and HOB combinations were grown in serum vials to identify the best-performing ones. We observed synergistic effects on growth for several combinations, and in all combinations a co-culture consisting out of both HOB and MOB could be maintained during five days of cultivation. Relative to the axenic growth, five out of the ten co-cultures exhibited 1.1-3.8 times higher protein concentration and two combinations presented 2.4-6.1 times higher essential amino acid content. The MP produced in this study generally contained lower amounts of the essential amino acids histidine, lysine and threonine, compared to tofu and fishmeal. The most promising combination in terms of protein concentration and essential amino acid profile was Methyloparacoccus murrelli LMG 27482 with Cupriavidus necator LMG 1201. Microbial protein from M. murrelli and C. necator requires 27-67% less quantity than chicken, whole egg and tofu, while it only requires 15% more quantity than the amino acid-dense soybean to cover the needs of an average adult. In conclusion, while limitations still exist, the co-cultivation of MOB and HOB creates an alternative route for MP production leveraging safe and sustainably-produced gaseous substrates.

Assessment of the UV/Chlorine Process in the Disinfection of Pseudomonas aeruginosa: Efficiency and Mechanism

UV irradiation and chlorination have been widely used for water disinfection. However, there are some limitations, such as the risk of generating viable but nonculturable bacteria and bacteria reactivation when using UV irradiation or chlorination alone. This study comprehensively evaluated the feasibility of the UV/chlorine process in drinking water disinfection, and Pseudomonas aeruginosa was selected as the target microorganism. The number of culturable cells was effectively reduced by more than 5 orders of magnitude (5-log₁₀) after UV, chlorine, and UV/chlorine treatments. However, intact and VBNC cells were detected at 10³ to 10⁴ cells/mL after UV and chlorine treatments, whereas they were undetectable after UV/chlorine treatment due to the primary contribution of reactive chlorine species (Cl^•, Cl₂^•-, and ClO^•). After UV/chlorine treatment, the metabolic activity determined using single cell Raman spectroscopy was much lower than that after UV. The level of toxic opr gene in P. aeruginosa decreased by more than 99% after UV/chlorine treatment. Importantly, bacterial dark reactivation was completely suppressed by UV/chlorine treatment but not UV or chlorination. This study suggests that the UV/chlorine treatment can completely damage bacteria and is promising for pathogen inactivation to overcome the limitations of UV and chlorine treatments alone.

Clinical Autopsy of a Reverse Osmosis Membrane Module

The desalination of seawater using reverse osmosis membranes is an attractive solution to global freshwater scarcity. However, membrane performance is reduced by (bio)fouling. Membrane autopsies are essential for identifying the type of fouling material, and applying corrective measures to minimize membrane fouling. Information from full-scale membrane autopsies guiding improved plant operations is scant in the formal literature. In this case-study, a reverse osmosis membrane from a full-scale seawater desalination plant with a feed channel pressure drop increase of about 218% over the pressure vessel was autopsied. The simultaneous determination of microbial cells, ATP, and total organic carbon (TOC) abundances per membrane area allowed estimating the contributions of biofouling and organic fouling. The abundance of microbial cells determined by flow cytometry (up to 7 × 108 cells/cm2), and ATP (up to 21,000 pg/cm2) as well as TOC (up to 98 μg/cm2) were homogeneously distributed on the membrane. Inorganic fouling was also measured, and followed a similar coverage distribution to that of biofouling. Iron (∼150 μg/cm2, estimated by ICP-MS) was the main inorganic foulant. ATR-FTIR spectra supported that membrane fouling was both organic/biological and inorganic. High-resolution SEM-EDS imaging of cross-sectioned membranes allowed assessing the thickness of the fouling layer (up to 20 μm) and its elemental composition. Imaging results further supported the results of homogeneous fouling coverage. Moreover, imaging revealed both zones with and without compression of the polysulfone membrane layer, suggesting that the stress due to operating pressure was heterogeneous. The procedure for this membrane autopsy provided a reasonable overview of the diverse contributors of fouling and might be a starting point to building a consensus autopsy protocol. Next, it would be valuable to build a RO membrane autopsy database, which can be used as a guidance and diagnostic tool to improve the management and operation of RO desalination plants.

Bacterial dynamics in drinking water distribution systems and flow cytometry monitoring scheme optimization

Water biostability is desired within drinking water distribution systems (DWDSs) to limit microbiologically-related operational, aesthetic and, eventually, health-related issues. However, variations in microbiological quality can take place both spatially along DWDS pipelines and temporally at single locations due to biofilm detachment, water quality seasonality and other processes. In this study, long- and short-term trends of bacterial concentration and community structure were investigated in a secondary branch of an unchlorinated DWDS for several months using high-frequency flow cytometry (FCM) and traditional laboratory monitoring campaigns. Long-term trends of bacterial concentrations and community structures were likely caused by changes in the water physical-chemical quality (i.e. pH and conductivity). Short-term daily pattern, instead, resulted in significant variations between the bacterial concentrations and community structures at different hours, likely due to biofilm detachment and loose deposits resuspension related to changes in the local water flow. These patterns, however, showed broad variations and did not persist during the entire monitoring campaign presumably due to the stochasticity of local instantaneous demand and seasonal changes in water consumption. During periods without sensible long-term trends, the sampling hours explain a comparable or larger fraction of the bacterial community diversity compared to dates. The variations observed with FCM were poorly or not detected by traditional laboratory analyses, as the correlation between the two were rather weak, highlighting the limited information provided by traditional approaches. On the other hand, FCM data correlated with water pH and conductivity, underlining the relation between physical-chemical and microbiological water quality. Such results suggest that the advanced control of the physical-chemical water quality could minimize the microbiological water quality variations. Moreover, monitoring campaign planning should take into account the sampling time to reduce the noise caused by daily fluctuations and/or assess the overall quality variations. Finally, as monitoring costs are one of the barriers which prevent a more widespread use of FCM, a monitoring scheme optimization strategy was developed. Such strategy employs the data from an initial high-frequency sampling period to select the sampling hours which maximize the observed variations of bacterial concentration and community composition.

Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir

Groundwater is a key resource for safe drinking water supply. Yet unconfined aquifers can be vulnerable to microbial contamination during extreme weather events that lead to surface runoff. The current study characterises the groundwater microbiome of a porous basaltic rock aquifer in South-West Iceland used for drinking water extraction and analyses the microbial community dynamics during surface runoff. The groundwater microbial community sampled from 12 wells across the extraction area contained over 745 prokaryotic genera and was phylogenetically similar between wells and most seasons, representing a diverse but homogenous ecosystem. The largest seasonal variation in the microbial community composition was detected during a period of concurrent snow melt and high precipitation leading to surface runoff. This period was characterised by an increased abundance of soil-associated taxa in the groundwater microbiome and specifically of taxa assigned to Aeromonas and Bacillus. A field experiment simulating high surface runoff around a groundwater well confirmed the increased abundance of surface soil microorganisms in the well water, indicating vulnerability of groundwater towards surface microbial intrusion during extreme weather events. As such events are likely to increase due to climate change, novel water management tools such as microbial community analysis could help ensure drinking water safety.

Characteristics of biostability of drinking water in aged pipes after water source switching: ATP evaluation, biofilms niches and microbial community transition

Delivering quality-changed water often contributes to the biological instability of drinking water distribution systems (DWDS). However, the potential effects of quality-changed water on the biostability within DWDS are not well understood, especially after water switching to quality-improved water. The objective of this study was to investigate the effects of quality-improved water on DWDS, focusing on the stability of biofilm. The practical aged-pipe was assembled into pipe reactors to simulate the effect of switching to quality-improve water. The adenosine triphosphate (ATP) concentration of bulk water in the pipe reactors increased from ∼1.2 ng/L to almost above 5 ng/L when fed water switching to TP 2. Biomass quantified by measuring ATP concentration confirmed that the risk of biofilm release through aged cast-iron (CI) pipe surfaces after water source switching. The changes in water characteristics due to quality-improved water source could cause bacteria release in DWDS at the initial period (at the first 7 days). However, the DWDS can establish the new stable phase after 42 days. Over time, biomass in the bulk water of the distribution system decreased significantly (The ATP concentration in the bulk maintains around 3 ng/L) after 42 days, indicating the improvement of water quality. The biofilm was dominated by bacteria related to iron-cycling process, and at the genus level, Desulfovibrio had the highest relative abundance, however, it decreased significantly (from 48% to 9.3%) after water source switching. And there was a slightly increase in the fraction of iron-oxidizing bacteria (IOB) and siderophore-producing bacteria (SPB), but a relatively higher increase in nitrate-reducing bacteria (NRB), nitrobacteria (NOB), and iron-reducing bacteria (IRB) was observed. Taken together, these results and the corrosion morphology, indicate that pipe biofilm and corrosion were chemically and microbially stable after re-stability under water source switching. In addition, the bulk water environment showed a marked decrease in selected bacteria at genus level, including pathogenic species, indicating the improvement of quality in drinking water.

A palette of fluorophores that are differentially accumulated by wild-type and mutant strains of Escherichia coli: surrogate ligands for profiling bacterial membrane transporters

Our previous work demonstrated that two commonly used fluorescent dyes that were accumulated by wild-type Escherichia coli MG1655 were differentially transported in single-gene knockout strains, and also that they might be used as surrogates in flow cytometric transporter assays. We summarize the desirable properties of such stains, and here survey 143 candidate dyes. We eventually triage them (on the basis of signal, accumulation levels and cost) to a palette of 39 commercially available and affordable fluorophores that are accumulated significantly by wild-type cells of the 'Keio' strain BW25113, as measured flow cytometrically. Cheminformatic analyses indicate both their similarities and their (much more considerable) structural differences. We describe the effects of pH and of the efflux pump inhibitor chlorpromazine on the accumulation of the dyes. Even the 'wild-type' MG1655 and BW25113 strains can differ significantly in their ability to take up such dyes. We illustrate the highly differential uptake of our dyes into strains with particular lesions in, or overexpressed levels of, three particular transporters or transporter components (yhjV, yihN and tolC). The relatively small collection of dyes described offers a rapid, inexpensive, convenient and informative approach to the assessment of microbial physiology and phenotyping of membrane transporter function.

Computational Analysis of Microbial Flow Cytometry Data

Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.