Flow cytometry applications in water treatment, distribution, and reuse: A review

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.

Efficacy and Mechanism of Antibiotic Resistance Gene Degradation and Cell Membrane Damage during Ultraviolet Advanced Oxidation Processes

Combinations of UV with oxidants can initiate advanced oxidation processes (AOPs) and enhance bacterial inactivation. However, the effectiveness and mechanisms of UV-AOPs in damaging nucleic acids (e.g., antibiotic resistance genes (ARGs)) and cell integrity represent a knowledge gap. This study comprehensively compared ARG degradation and cell membrane damage under three different UV-AOPs. The extracellular ARG (eARG) removal efficiency followed the order of UV/chlorine > UV/H2O2 > UV/peracetic acid (PAA). Hydroxyl radical (•OH) and reactive chlorine species (RCS) largely contributed to eARG removal, while organic radicals made a minor contribution. For intracellular ARGs (iARGs), UV/H2O2 did not remove better than UV alone due to the scavenging of •OH by cell components, whereas UV/PAA provided a modest synergism, likely due to diffusion of PAA into cells and intracellular •OH generation. Comparatively, UV/chlorine achieved significant synergistic iARG removal, suggesting the critical role of the RCS in resisting cellular scavenging and inactivating ARGs. Additionally, flow cytometry analysis demonstrated that membrane damage was mainly attributed to chlorine oxidation, while the impacts of radicals, H2O2, and PAA were negligible. These results provide mechanistic insights into bacterial inactivation and fate of ARGs during UV-AOPs, and shed light on the suitability of quantitative polymerase chain reaction (qPCR) and flow cytometry in assessing disinfection performance.

Automated identification of toxigenic cyanobacterial genera for water quality control purposes

Cyanobacteria are the dominating microorganisms in aquatic environments, posing significant risks to public health due to toxin production in drinking water reservoirs. Traditional water quality assessments for abundance of the toxigenic genera in water samples are both time-consuming and error-prone, highlighting the urgent need for a fast and accurate automated approach. This study addresses this gap by introducing a novel public dataset, TCB-DS (Toxigenic Cyanobacteria Dataset), comprising 2593 microscopic images of 10 toxigenic cyanobacterial genera and subsequently, an automated system to identify these genera which can be divided into two parts. Initially, a feature extractor Convolutional Neural Network (CNN) model was employed, with MobileNet emerging as the optimal choice after comparing it with various other popular architectures such as MobileNetV2, VGG, etc. Secondly, to perform classification algorithms on the extracted features of the first section, multiple approaches were tested and the experimental results indicate that a Fully Connected Neural Network (FCNN) had the optimal performance with weighted accuracy and f1-score of 94.79% and 94.91%, respectively. The highest macro accuracy and f1-score were 90.17% and 87.64% which were acquired using MobileNetV2 as the feature extractor and FCNN as the classifier. These results demonstrate that the proposed approach can be employed as an automated screening tool for identifying toxigenic Cyanobacteria with practical implications for water quality control replacing the traditional estimation given by the lab operator following microscopic observations. The dataset and code of this paper are publicly available at https://github.com/iman2693/CTCB.

Back to the future: Comparing yeast as an outmoded artificial tracer for simulating microbial transport in karst aquifer systems to more modern approaches

Bacterial contamination of karst groundwater is a major concern for public health. Artificial tracing studies are crucial for establishing links between locations where pollutants can rapidly reach the aquifer systems and subsequent receptors, as well as for enhanced understanding of pollutant transport. However, widely used solute artificial tracers do not always move through the subsurface in the same manner as particles and microorganisms, hence may not be ideal proxies for predicting movement of bacterial contaminants. This study evaluates whether a historically used microbial tracer (yeast) which is readily available, inexpensive, and environmentally friendly, but usually overlooked in modern karst hydrogeological studies due to challenges associated with its detection and quantification in the past, can reemerge as a valuable tracer using the latest technology for its detection. Two field-based studies on separate karst systems were carried out during low-flow conditions using a portable particle counter along with flow cytometry measurements to monitor the recovery of the yeast at the springs. Soluble fluorescent dyes were also injected simultaneously with the yeast for comparison of transport dynamics. On one tracer test, through a karst conduit of much higher velocities, the injected yeast and fluorescent dye arrived at the same time at the spring, in comparison to the tracer test on a conduit system with lower groundwater velocities in which the yeast particles were detected before the dye at the sampling site. Both a portable particle counter and flow cytometry successfully detected yeast during both tests, thereby demonstrating the applicability of this tracer with contemporary instrumentation. Even though no significant advantages of flow cytometry over the portable counter system can be reported on the basis of the presented results, this study has shown that flow cytometry can be successfully used to detect and quantify introduced microbial tracers in karst environments with extremely high precision.

Recent advances in microfluidic-based spectroscopic approaches for pathogen detection

Rapid identification of pathogens with higher sensitivity and specificity plays a significant role in maintaining public health, environmental monitoring, controlling food quality, and clinical diagnostics. Different methods have been widely used in food testing laboratories, quality control departments in food companies, hospitals, and clinical settings to identify pathogens. Some limitations in current pathogens detection methods are time-consuming, expensive, and laborious sample preparation, making it unsuitable for rapid detection. Microfluidics has emerged as a promising technology for biosensing applications due to its ability to precisely manipulate small volumes of fluids. Microfluidics platforms combined with spectroscopic techniques are capable of developing miniaturized devices that can detect and quantify pathogenic samples. The review focuses on the advancements in microfluidic devices integrated with spectroscopic methods for detecting bacterial microbes over the past five years. The review is based on several spectroscopic techniques, including fluorescence detection, surface-enhanced Raman scattering, and dynamic light scattering methods coupled with microfluidic platforms. The key detection principles of different approaches were discussed and summarized. Finally, the future possible directions and challenges in microfluidic-based spectroscopy for isolating and detecting pathogens using the latest innovations were also discussed.

Flow cytometric assessments of metabolic activity in bacterial assemblages provide insight into ecosystem condition along the Buffalo National River, Arkansas

The Buffalo National River (BNR), on karst terrain in Arkansas, is considered an extraordinary water resource. Water collected in Spring 2017 along BNR was metagenomically analyzed using 16S rDNA, and for 17 months (5/2017-11/2018), bacterial responses were measured in relation to nutrients sampled along a stretch of BNR near a concentrated animal feed operation (CAFO) on Big Creek. Because cell count and esterase activity can increase proportionally with organic enrichment, they were hypothesized to be elevated near the CAFO. Counts (colony forming units; CFUs) were different among sites for 73 % of the months; Big Creek generated highest CFUs 27 % of the time, with the closest downstream site at 13.3 %. Esterase activity was different among sites 94 % of the time, with Big Creek exhibiting lowest activity 71 % of the time. Over the months, activity was similar across sites at ~70 % active, except at Big Creek (56 %). The α-diversity of BNR microbial consortia near a wastewater treatment plant (WWTP) and the CAFO was related to distance from the WWTP and CAFO. The inverse relationship between high CFUs and low esterase activity at Big Creek (r = -0.71) actuated in vitro exposures of bacteria to organic wastewater contaminants (OWC) previously identified in the watershed. Exponential-phase Escherichia coli (stock strain), Streptococcus suis (avirulent, from swine), and S. dysgalactiae (virulent, from silver carp, Hypophthalmichthys molitrix) were incubated with atrazine, pharmaceuticals (17 α-ethynylestradiol and trenbolone), and antimicrobials (tylosin and butylparaben). Bacteria were differentially responsive. Activity varied with exposure time and OWC type, but not concentration; atrazine decreased it most. Taken together - the metagenomic taxonomic similarities along BNR, slightly higher bacterial growth and lower bacterial esterase at the CAFO, and the lab exposures of bacterial strains showing that OWC altered metabolism - the results indicated that bioactive OWC entering the watershed can strongly influence microbial processes in the aquatic ecosystem.

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.

Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems

Reductions in nonresidential water demand during the COVID-19 pandemic highlighted the importance of understanding how water age impacts drinking water quality and microbiota in piped distribution systems. Using benchtop model distribution systems, we aimed to characterize the impacts of elevated water age on microbiota in bulk water and pipe wall biofilms. Five replicate constant-flow reactors were fed with municipal chloraminated tap water for 6 months prior to building closures and 7 months after. After building closures, chloramine levels entering the reactors dropped; in the reactor bulk water and biofilms the mean cell counts and ATP concentrations increased over an order of magnitude while the detection of opportunistic pathogens remained low. Water age, and the corresponding physicochemical changes, strongly influenced microbial abundance and community composition. Differential initial microbial colonization also had a lasting influence on microbial communities in each reactor (i.e., historical contingency).

An optimized PDMS microfluidic device for ultra-fast and high-throughput imaging flow cytometry

Imaging flow cytometry (IFC) is a powerful tool for cell detection and analysis due to its high throughput and compatibility in image acquisition. Optical time-stretch (OTS) imaging is considered as one of the most promising imaging techniques for IFC because it can realize cell imaging at a flow speed of around 60 m s-1. However, existing PDMS-based microchannels cannot function at flow velocities higher than 10 m s-1; thus the capability of OTS-based IFC is significantly limited. To overcome the velocity barrier for PDMS-based microchannels, we proposed an optimized design of PDMS-based microchannels with reduced hydraulic resistance and 3D hydrodynamic focusing capability, which can drive fluids at an ultra-high flow velocity (of up to 40 m s-1) by using common syringe pumps. To verify the feasibility of our design, we fabricated and installed the microchannel in an OTS IFC system. The experimental results first proved that the proposed microchannel can support a stable flow velocity of up to 40 m s-1 without any leakage or damage. Then, we demonstrated that the OTS IFC is capable of imaging cells at a velocity of up to 40 m s-1 with good quality. To the best of our knowledge, it is the first time that IFC has achieved such a high flow velocity just by using a PDMS-glass chip. Moreover, high velocity can enhance the focusing of cells on the optical focal plane, increasing the number of detected cells and the throughput. This work provides a promising solution for IFC to fully release its capability of advanced imaging techniques by operating at an extremely high screening throughput.

Portable impedance-sensing device for microorganism characterization in the field

A variety of biosensors have been proposed to quickly detect and measure the properties of individual microorganisms among heterogeneous populations, but challenges related to cost, portability, stability, sensitivity, and power consumption limit their applicability. This study proposes a portable microfluidic device based on impedance flow-cytometry and electrical impedance spectroscopy that can detect and quantify the size of microparticles larger than 45 µm, such as algae and microplastics. The system is low cost ($300), portable (5 cm [Formula: see text] 5 cm), low-power (1.2 W), and easily fabricated utilizing a 3D-printer and industrial printed circuit board technology. The main novelty we demonstrate is the use of square wave excitation signal for impedance measurements with quadrature phase-sensitive detectors. A linked algorithm removes the errors associated to higher order harmonics. After validating the performance of the device for complex impedance models, we used it to detect and differentiate between polyethylene microbeads of sizes between 63 and 83 µm, and buccal cells between 45 and 70 µm. A precision of 3% is reported for the measured impedance and a minimum size of 45 µm is reported for the particle characterization.

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.

Service-lines as major contributor to water quality deterioration at customer ends

Biofilm detachment contributes to water quality deterioration. However, the contributions of biofilm detachment from different pipes have not been quantified or compared. Following the introduction of partial reverse osmosis (RO) in drinking water production, this study analyzed particles at customers' ends and tracked their origins to water distribution mains and service lines. For doing so, filter bags were installed in front of water meters to capture upstream detached particles, while biofilm from water main and service line were sampled by cutting pipe specimens. The results showed that elemental concentrations of the biofilm in mains were higher than those of service lines (54.3-268.5 vs. 27.1-44.4 μg/cm²), both dominated by Ca. Differently, filter bags were dominated by Fe/Mn (77.5-98.1%). After introducing RO, Ca significantly decreased in biofilms of mains but not service lines, but the released Fe/Mn rather than Ca arrived at customers' ends. The ATP concentrations of service lines were higher than mains, which decreased on mains but increased in service lines after introducing RO. For the core ASVs, 13/24 were shared by service lines (17), mains (21), and filter bags (17), which were assigned mainly to Nitrospira spp., Methylomagnum spp., Methylocytis spp., and IheB2-23 spp. According to source tracking results, service lines contributed more than mains to the particulate material collected by filter bags (57.6 ± 13.2% vs. 13.0 ± 11.6%). To the best of our knowledge, the present study provides the first evidence of service lines' direct and quantitative contributions to potential water quality deterioration at customers' ends. This highlights the need for the appropriate management of long-neglected service line pipes, e.g., regarding material selection, length optimization, and proper regulation.

A new workflow for assigning removal credits to assess overall performance of managed aquifer recharge (MAR)

Pathogen removal in managed aquifer recharge (MAR) systems is dependent upon numerous operational, physicochemical water quality, and biological parameters. Due to the site-specific conditions affecting these parameters, guidelines for specifying pathogen removal have historically taken rather precautionary and conservative approaches in order to protect groundwater quality and public health. A literature review of regulated pathogens in MAR applications was conducted and compared to up-and-coming indicators and surrogates for pathogen assessment, all of which can be gathered into a toolbox from which regulators and operators alike can select appropriate pathogens for monitoring and optimization of MAR practices. Combined with improved knowledge of pathogen fate and transport obtained through lab- and pilot-scale studies and supported by modeling, this foundation can be used to select appropriate, site-specific pathogens for regarding a more efficient pathogen retention, ultimately protecting public health and reducing costs. This paper outlines a new 10 step-wise workflow for moving towards determining robust removal credits for pathogens based on risk management principles. This approach is tailored to local conditions while reducing overly conservative regulatory restrictions or insufficient safety contingencies. The workflow is intended to help enable the full potential of MAR as more planned water reuse systems are implemented in the coming years.

Effect of NaClO and ClO2 on the bacterial properties in a reclaimed water distribution system: efficiency and mechanisms

Extensive application of reclaimed water alleviated water scarcity obviously. Bacterial proliferation in reclaimed water distribution systems (RWDSs) poses a threat to water safety. Disinfection is the most common method to control microbial growth. The present study investigated the efficiency and mechanisms of two widely used disinfectants: sodium hypochlorite (NaClO) and chlorine dioxide (ClO₂) on the bacterial community and cell integrity in effluents of RWDSs through high-throughput sequencing (Hiseq) and flow cytometry, respectively. Results showed that a low disinfectant dose (1 mg/L) did not change the bacterial community basically, while an intermediate disinfectant dose (2 mg/L) reduced the biodiversity significantly. However, some tolerant species survived and multiplied in high disinfectant environments (4 mg/L). Additionally, the effect of disinfection on bacterial properties varied between effluents and biofilm, with changes in the abundance, bacterial community, and biodiversity. Results of flow cytometry showed that NaClO disturbed live bacterial cells rapidly, while ClO₂ caused greater damage, stripping the bacterial membrane and exposing the cytoplasm. This research will provide valuable information for assessing the disinfection efficiency, biological stability control, and microbial risk management of reclaimed water supply systems.

Can online particle counters and electrochemical sensors distinguish normal periodic and aperiodic drinking water quality fluctuations from contamination?

Early warning systems monitoring the quality of drinking water need to distinguish between normal quality fluctuations and those caused by contaminants. Thus, to decrease the number of false positive events, normal water quality fluctuations, whether periodic or aperiodic, need to be characterized. For this, we used a novel flow-imaging particle counter, a light-scattering particle counter, and electrochemical sensors to monitor the drinking water quality of a pressure zone in a building complex for 109 days. Data were analyzed to determine the feasibility of the sensors and particle counters to distinguish periodic and aperiodic fluctuations from real-life contaminants. The concentrations of particles smaller than 10 μm and N, Small, Large, and B particles showed sudden changes recurring daily, likely due to the flow rate changes in the building complex. Conversely, the concentrations of larger than 10 μm particles and C particles, in addition to the responses of electrochemical sensors, remained in their low typical values despite flow rate changes. The aperiodic events, likely resulting from an abnormally high flow rate in the water mains due to maintenance, were detected using particle counters and electrochemical sensors. This study provides insights into choosing water quality sensors by showing that machine learning-based particle classes, such as B, C, F, and particles larger than 10 μm are promising in distinguishing contamination from aperiodic and periodic fluctuations while the use of other particle classes and electrochemical sensors may require dynamic baseline to decrease false positive events in an early warning system.

Rapid Detection of the Activity of Lacticaseibacillus Casei Zhang by Flow Cytometry

Food processing, e.g., freeze-drying, exerts strong pressure on bacteria in the food matrix, decreasing their viability/activity and even forcing them to become viable but unculturable (VBNC), which are often underestimated by traditional plate count. The strict standards of bacterial viability in probiotic products require accurate cell viability/activity enumeration. We developed a staining (5(6)-carboxyfluorescein diacetate succinimide ester, propidium iodide)-based flow cytometry rapid method for detecting the viability/activity of Lacticaseibacillus (Lb.) casei Zhang, a widely used probiotic in the dairy industry in China. We optimized the procedural and instrumental parameters for generating results comparable to that of standard plate counts. This method was also applied to freeze-dried Lb. casei Zhang, yielding 7.7 × 1011 CFU/g, which was non-significantly higher than the results obtained by plate count (6.4 × 1011 CFU/g), possibly due to the detection of VBNC cells in the freeze-dried powder. We anticipated that this method can be used for detecting lactic acid bacteria in other probiotic food/beverages.

Multiple fluorescence approaches to identify rapid changes in microbial indicators at karst springs

Karst springs are globally important for drinking water supply but are often also exceptionally vulnerable to contamination. Such springs usually exhibit strong variation in microbial water quality in sharp response to rainfall events, thus, posing a health hazard to consumers of water supplied from these sources. The rapid detection of such changes is extremely important as well as being able to establish a link to the sources of such pollution, so that appropriate measures can be taken both in terms of immediate protection of human health and the management of karst aquifers. In this study, a fluorescence-based multi-parameter approach was trialed in order to evaluate which methods can be used to monitor rainfall-induced rapid changes in microbial water quality at karst springs, as well as determine whether such changes can be linked to sources of human effluent contamination. The results from three monitoring periods at two karst springs revealed marked responses to rainfall events for all of the microbial parameters measured. Total cell count (TCC) measurements using flow cytometry (FCM) showed very strong positive correlations with the more conventionally monitored faecal indicator bacteria (FIB) and total coliforms (TC), indicating that such a fluorescence-based and cultivation-independent technique can be very useful to indicate rapid changes in microbial water quality at karst springs. Furthermore, very strong positive correlations were also found between tryptophan-like fluorescence (TLF) measurements and concentrations of all monitored microbial parameters, again demonstrating that such a fluorescence-based approach can also be useful for detecting rapid changes in concentrations of traditional faecal indicators. Interestingly, it was found that fluorescent whitening compounds (FWCs) signals do not necessarily follow temporal variations of microbial indicators. However, the frequency of detection of positive FWCs signals may still reveal useful information about the overall magnitude of human wastewater effluent impacts on karst aquifer systems.

Leave No Trace? Ecological and anthropogenic determinants of antibiotic resistant bacteria in a recreational alpine environment

Antibiotic resistant bacteria (ARB) have been detected in remote environments, but the degree to which their presence is due to anthropogenic contamination remains unclear. Here, anthropogenic and ecological determinants of ARB were characterized in remote and highly visited areas of Rocky Mountain National Park in the United States. Soil and water samples were collected from 29 sites once a month for three months and measured for bacteria resistant to seven antibiotics with flow cytometry. A novel index of the likelihood of human presence (HPI) was generated for estimating human impact on ARB abundance. The HPI accounted for 44% of variation in ARB abundance in water samples (p < 0.0001) and 51% of variation in soil samples (p < 0.00001). Human presence index was illustrated as a reliable predictor of ARB abundance despite a tendency to underpredict at higher levels of human impact. Ecological determinants such as temperature, elevation, slope, and aspect were also found to be significantly associated with ARB abundance. These findings suggest that human presence drives the abundance of ARB in Rocky Mountain National Park, but ecological variables play a significant role in their presence and dispersal.

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.

Coliphages as viral indicators of sanitary significance for drinking water

Coliphages are virus that infect coliform bacteria and are used in aquatic systems for risk assessment for human enteric viruses. This mini-review appraises the types and sources of coliphage and their fate and behavior in source waters and engineered drinking water treatment systems. Somatic (cell wall infection) and F+ (male specific) coliphages are abundant in drinking water sources and are used as indicators of fecal contamination. Coliphage abundances do not consistently correlate to human enteric virus abundance, but they suitably reflect the risks of exposure to human enteric viruses. Coliphages have highly variable surface characteristics with respect to morphology, size, charge, isoelectric point, and hydrophobicity which together interact to govern partitioning and removal characteristics during water treatment. The groups somatic and F+ coliphages are valuable for investigating the virus elimination during water treatment steps and as indicators for viral water quality assessment. Strain level analyses (e.g., Qβ or GA-like) provide more information about specific sources of viral pollution but are impractical for routine monitoring. Consistent links between rapid online monitoring tools (e.g., turbidity, particle counters, and flow cytometry) and phages in drinking water have yet to be established but are recommended as a future area of research activity. This could enable the real-time monitoring of virus and improve the process understanding during transient operational events. Exciting future prospects for the use of coliphages in aquatic microbiology are also discussed based on current scientific evidence and practical needs.

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.

The status of potable water reuse implementation

A review of the current status of direct and indirect potable water reuse (DPR/IPR) implementation has been conducted, focusing on the regulatory and practical aspects and with reference to the most recent published literature. The review encompasses (a) the principal contaminant types, their required removal and the methods by which their concentration is monitored, (b) regulatory approaches and stipulations in assessing/ratifying treatment schemes and maintaining treated water quality, and (c) existing full-scale installations. Analytical methods discussed include established in-line monitoring tools, such as turbidity measurement, to more recent polymerase chain reaction (PCR)-based assay methods for microbial detection. The key risk assessment tools of quantitative microbial risk assessment (QMRA) and water safety plans (WSPs) are considered in relation to their use in selecting/ratifying treatment schemes, and the components of the treatment schemes from 40 existing IPR/DPR installations summarised. Five specific schemes are considered in more detail. The review reveals:Whilst there are a number of ongoing projects where RO is not used because of the challenge imposed by disposal of RO concentrate, the prevalence of the sequential RO-UV combination implies the importance of quantifying the impact of process upsets on these unit operations.

Flow Cytometry and Fecal Indicator Bacteria Analyses for Fingerprinting Microbial Pollution in Karst Aquifer Systems

Microbial pollution of aquifers is a persistent water quality problem globally which poses significant risks to public health. Karst aquifer systems are exceptionally vulnerable to pollution from fecal contamination sources as a result of rapid recharge of water from the surface via discrete pathways linked to highly conductive, solutionally enlarged conduits alongside strong aquifer heterogeneity. Consequently, rapid changes in microbial water quality, which are difficult to monitor with expensive and time-consuming conventional microbiological methods, are a major concern in karst environments. This study examined flow cytometric (FCM) fingerprinting of bacterial cells in groundwater together with fecal indicator bacteria (FIB) at nine separate karst springs of varying catchment size over a 14 month period in order to assess whether such a technique can provide faster and more descriptive information about microbial pollution through such karst aquifer systems. Moreover, the data have also been evaluated with respect to the potential of using turbidity as an easy-to-measure proxy indicator of microbial pollution in a novel way. We argue that FCM provides additional data from which enhanced insights into fecal pollution sources and its fate and transport in such karst catchments can be gained. We also present valuable new information on the potential and limitations of turbidity as an indicator of fecal groundwater contamination in karst. FCM has the potential to become a more widely used tool in the field of contaminant hydrogeology.

An online flow-imaging particle counter and conventional water quality sensors detect drinking water contamination in the presence of normal water quality fluctuations

Contamination detection in drinking water is crucial for water utilities in terms of public health; however, current online water quality sensors can be unresponsive to various possible contaminants consisting of particulate and dissolved content or require a constant supply of reagents and sample preparation. We used a two-line test environment connected to a drinking water distribution system with flow-imaging particle counters and conventional sensors to assess their responses to the injection of contaminants into one line, including stormwater, treated wastewater, wastewater, well water, and Escherichia coli, while simultaneously measuring responses to normal water quality fluctuations in the other line. These water quality fluctuations were detected with all of the conventional sensors (except conductivity) and with 3 out of 5 of the size- and shape-derived particle classes of the flow-imaging particle counter. The flow-imaging particle counter was able to detect all of the studied contaminants, e.g. municipal wastewater at 0.001% (v/v), while the oxidation-reduction potential sensor outperformed other conventional sensors, detecting the same wastewater at 0.03% (v/v). The presence of particles less than 1 µm in size was shown to be a generic parameter for the detection of particulates present in the studied contaminants; however, they manifested a considerable response to fluctuations which led to lower relative response to contaminants in comparison to larger particles. The particle size and class distributions of contaminants were different from those of drinking water, and thus monitoring particles larger than 1 µm or specific particle classes of flow-imaging particle counter, which are substantially more abundant in contaminated water than in pure drinking water, can improve the detection of contamination events. Water utilities could optimize contamination detection by selecting water quality parameters with a minimal response to quality fluctuations and/or a high relative response to contaminants.

Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse

Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.

A review of microscopic cell imaging and neural network recognition for synergistic cyanobacteria identification and enumeration

Real-time cyanobacteria/algal monitoring is a valuable tool for early detection of harmful algal blooms, water treatment efficacy evaluation, and assists tailored water quality risk assessments by considering taxonomy and cell counts. This review evaluates and proposes a synergistic approach using neural network image recognition and microscopic imaging devices by first evaluating published literature for both imaging microscopes and image recognition. Quantitative phase imaging was considered the most promising of the investigated imaging techniques due to the provision of enhanced information relative to alternatives. This information provides significant value to image recognition neural networks, such as the convolutional neural networks discussed within this review. Considering published literature, a cyanobacteria monitoring system and corresponding image processing workflow using in situ sample collection buoys and on-shore sample processing was proposed. This system can be implemented using commercially available equipment to facilitate accurate, real-time water quality monitoring.

Graphical abstract

Lab experiments on hybridization of managed aquifer recharge with river water via sand column, pre-oxidation, and nanofiltration

A hybridization of managed aquifer recharge (MAR) with pre-oxidation processes was conducted in this study to investigate changes in dissolved organic matter characteristics and the attenuation of selected trace organic contaminants (TrOCs). Potassium permanganate, chlorine, and ozone treatments were used for pre-oxidation, which effectively attenuated some TrOCs, particularly the combination of MAR with ozone achieved 84-99% attenuation. The pre-oxidation step using potassium permanganate showed high removal of carbamazepine (96%). Moreover, MAR was also combined with nanofiltration (NF) as a multi-barrier concept for the removal of persistent TrOCs after MAR. A short-chain polyfluoroalkyl substance (PFAS) was effectively removed after combining MAR columns with NF membranes. Thus, pre-oxidation coupled with MAR followed by NF could potentially enhance the removal of selected TrOCs.

Flow Cytometric Analysis of Bacterial Protein Synthesis: Monitoring Vitality After Water Treatment

Bacterial vitality after water disinfection treatment was investigated using bio-orthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM). Protein synthesis activity and DNA integrity (BONCAT–SYBR Green) was monitored in Escherichia coli monocultures and in natural marine samples after UV irradiation (from 25 to 200 mJ/cm²) and heat treatment (from 15 to 45 min at 55°C). UV irradiation of E. coli caused DNA degradation followed by the decrease in protein synthesis within a period of 24 h. Heat treatment affected both DNA integrity and protein synthesis immediately, with an increased effect over time. Results from the BONCAT method were compared with results from well-known methods such as plate counts (focusing on growth) and LIVE/DEAD™ BacLight™ (focusing on membrane permeability). The methods differed somewhat with respect to vitality levels detected in bacteria after the treatments, but the results were complementary and revealed that cells maintained metabolic activity and membrane integrity despite loss of cell division. Similarly, analysis of protein synthesis in marine bacteria with BONCAT displayed residual activity despite inability to grow or reproduce. Background controls (time zero blanks) prepared using different fixatives (formaldehyde, isopropanol, and acetic acid) and several different bacterial strains revealed that the BONCAT protocol still resulted in labeled, i.e., apparently active, cells. The reason for this is unclear and needs further investigation to be understood. Our results show that BONCAT and FCM can detect, enumerate, and differentiate bacterial cells after physical water treatments such as UV irradiation and heating. The method is reliable to enumerate and explore vitality of single cells, and a great advantage with BONCAT is that all proteins synthesized within cells are analyzed, compared to assays targeting specific elements such as enzyme activity.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

Stagnation leads to short-term fluctuations in the effluent water quality of biofilters: A problem for greywater reuse?

A key characteristic of decentralized greywater treatment and reuse is high variability in both nutrient concentrations and flow. This variability in flow leads to stagnant water in the system and causes short-term fluctuations in the effluent water quality. Automated monitoring tools provide data to understand the mechanisms underlying the dynamics and to adapt control strategies accordingly. We investigated the fluctuations in a building-scale greywater treatment system comprising a membrane bioreactor followed by a biological activated carbon filter. Short-term dynamics in the effluent of the biological activated carbon filter were monitored with automated flow cytometry and turbidity, and the impact of these fluctuations on various hygiene-relevant parameters in the reuse water was evaluated. Continuous biofilm detachment into the stagnant water in the biological activated carbon filter led to temporarily increased turbidity and cell concentrations in the effluent after periods of stagnation. The fluctuations in cell concentrations were consistent with a model assuming higher detachment rates during flow than during times with stagnant water. For this system, total cell concentration and turbidity were strongly correlated. We also showed that the observed increase in cell concentration was not related to either an increase of organic carbon concentration or the concentration of two opportunistic pathogens, P. aeruginosa and L. pneumophila. Our findings demonstrate that turbidity measurements are sensitive to changes in the effluent water quality and can be used to monitor the fluctuations caused by intermittent flow. Intermittent flow did not lead to an increase in opportunistic pathogens, and this study provides no indications that stagnant water in biological activated carbon filters need be prevented.

Precision early detection of invasive and toxic cyanobacteria: A case study of Raphidiopsis raciborskii

Blooms of the toxic cyanobacterium, Raphidiopsis raciborskii (basionym Cylindrospermopsis raciborskii), are becoming a major environmental issue in freshwater ecosystems globally. Our precision prevention and early detection of R. raciborskii blooms rely upon the accuracy and speed of the monitoring method. A duplex digital PCR (dPCR) monitoring approach was developed and validated to detect the abundance and toxin-producing potential of R. raciborskii simultaneously in both laboratory spiked and environmental samples. Results of dPCR were strongly correlated with traditional real time quantitative PCR (qPCR) and microscopy for both laboratory and environmental samples. However, discrepancies between methods were observed when measuring R. raciborskii at low abundance (1 - 10⁵ cells L ^- 1), with dPCR showing a higher precision compared to qPCR at low cell concentration. Furthermore, the dPCR assay had the highest detection rate for over two hundred environmental samples especially under low abundance conditions, followed by microscopy and qPCR. dPCR assay had the advantages of simple operation, time-saving, high sensitivity and excellent reproducibility. Therefore, dPCR would be a fast and precise monitoring method for the early warning of toxic bloom-forming cyanobacterial species and assessment of water quality risks, which can improve prediction and prevention of the impacts of harmful cyanobacterial bloom events in inland waters.

In-situ fluorescence spectroscopy is a more rapid and resilient indicator of faecal contamination risk in drinking water than faecal indicator organisms

Faecal indicator organisms (FIOs) are limited in their ability to protect public health from the microbial contamination of drinking water because of their transience and time required to deliver a result. We evaluated alternative rapid, and potentially more resilient, approaches against a benchmark FIO of thermotolerant coliforms (TTCs) to characterise faecal contamination over 14 months at 40 groundwater sources in a Ugandan town. Rapid approaches included: in-situ tryptophan-like fluorescence (TLF), humic-like fluorescence (HLF), turbidity; sanitary inspections; and total bacterial cells by flow cytometry. TTCs varied widely in six sampling visits: a third of sources tested both positive and negative, 50% of sources had a range of at least 720 cfu/100 mL, and a two-day heavy rainfall event increased median TTCs five-fold. Using source medians, TLF was the best predictor in logistic regression models of TTCs ≥10 cfu/100 mL (AUC 0.88) and best correlated to TTC enumeration (ρ_s 0.81), with HLF performing similarly. Relationships between TLF or HLF and TTCs were stronger in the wet season than the dry season, when TLF and HLF were instead more associated with total bacterial cells. Source rank-order between sampling rounds was considerably more consistent, according to cross-correlations, using TLF or HLF (min ρ_s 0.81) than TTCs (min ρ_s 0.34). Furthermore, dry season TLF and HLF cross-correlated more strongly (ρ_s 0.68) than dry season TTCs (ρ_s 0.50) with wet season TTCs, when TTCs were elevated. In-situ TLF or HLF are more rapid and resilient indicators of faecal contamination risk than TTCs.

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.

Online microbial monitoring of drinking water: How do different techniques respond to contaminations in practice?

Safeguarding the microbial water quality remains a challenge for drinking water utilities, and because of population growth and climate change, new issues arise regularly. To overcome these problems, biostable drinking water production and water reuse will become increasingly important. In this respect, high-resolution online microbial monitoring during treatment and distribution could prove essential. Here, we present the first scientific and practical comparison of multiple online microbial monitoring techniques in which six commercially available devices were set up in a full-scale drinking water production plant. Both the devices' response towards operational changes and contaminations, as well as their detection limit for different contaminations were evaluated and compared. During normal operation, all devices were able to detect abrupt operational changes such as backwashing of activated carbon filters and interruption of the production process in a fast and sensitive way. To benchmark their response to contaminations, the calculation of a dynamic baseline for sensitive separation between noise and events is proposed. In order of sensitivity, enzymatic analysis, ATP measurement, and flow cytometric fingerprinting were the most performant for detection of rain- and groundwater contaminations (0.01 - 0.1 v%). On the other hand, optical classification and flow cytometric cell counts showed to be more robust techniques, requiring less maintenance and providing direct information about the cell concentration, even though they were still more sensitive than plate counting. The choice for a certain technology will thus depend on the type of application and is a balance between sensitivity, price and maintenance. All things considered, a combination of several devices and use of advanced data analysis such as fingerprinting may be of added value. In general, the strategic implementation of online microbial monitoring as early-warning system will allow for intensive quality control by high-frequency sampling as well as a short event response timeframe.

Intermittent Water Supply Impacts on Distribution System Biofilms and Water Quality

Intermittent water supplies (IWS) are routinely experienced by drinking water distribution systems around the world, either due to ongoing operational practices or due to one off interruptions. During IWS events changing conditions may impact the endemic biofilms leading to hydraulic mobilisation of organic and inorganic materials attached to pipes walls with a resulting degradation in water quality. To study the impact of IWS on the microbiological and physico-chemical characteristics of drinking water, an experimental full-scale chlorinated pipe facility was operated over 60 days under realistic hydraulic conditions to allow for biofilm growth and to investigate flow resumption behaviour post-IWS events of 6, 48 and 144 hours. Turbidity and metal concentrations showed significant responses to flow restarting, indicating biofilm changes, with events greater than 6 hours generating more turbidity responses and hence discolouration risk. The increase in pressure when the system was restarted showed a substantial increase in total cell counts, while the subsequent increases in flow led to elevated turbidity and metals concentrations. SUVA₂₅₄ monitoring indicated that shorter times of non-water supply increased the risk of aromatic organic compounds and hence risk of disinfection-by-products formation. DNA sequencing indicated that increasing IWS times resulted in increased relative abundance of potential pathogenic microorganisms, such as Mycobacterium, Sphingomonas, and the fungi Penicillium and Cladosporium. Overall findings indicate that shorter IWS result in a higher proportion of aromatic organic compounds, which can potentially react with chlorine and increase risk of disinfection-by-products formation. However, by minimising IWS times, biofilm-associated impacts can be reduced, yet these are complex ecosystems and much remains to be understood about how microbial interactions can be managed to best ensure continued water safe supply.

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.

Machine learning issues and opportunities in ultrafast particle classification for label-free microflow cytometry

Machine learning offers promising solutions for high-throughput single-particle analysis in label-free imaging microflow cytomtery. However, the throughput of online operations such as cell sorting is often limited by the large computational cost of the image analysis while offline operations may require the storage of an exceedingly large amount of data. Moreover, the training of machine learning systems can be easily biased by slight drifts of the measurement conditions, giving rise to a significant but difficult to detect degradation of the learned operations. We propose a simple and versatile machine learning approach to perform microparticle classification at an extremely low computational cost, showing good generalization over large variations in particle position. We present proof-of-principle classification of interference patterns projected by flowing transparent PMMA microbeads with diameters of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${15.2}\,\upmu \text {m}$$\end{document}15.2μm and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${18.6}\,\upmu \text {m}$$\end{document}18.6μm. To this end, a simple, cheap and compact label-free microflow cytometer is employed. We also discuss in detail the detection and prevention of machine learning bias in training and testing due to slight drifts of the measurement conditions. Moreover, we investigate the implications of modifying the projected particle pattern by means of a diffraction grating, in the context of optical extreme learning machine implementations.

Opportunities for the application of real-time bacterial cell analysis using flow cytometry for the advancement of sterilization microbiology

Medical devices provide critical care and diagnostic applications through patient contact. Sterility assurance level (SAL) may be defined as the probability of a single viable micro-organism occurring on an item after a sterilization process. Sterilization microbiology often relies upon using an overkill validation method where a 12-log reduction in recalcitrant bacterial endospore population occurs during the process that exploits conventional laboratory-based culture media for enumeration. This timely review explores key assumptions underpinning use of conventional culture-based methods in sterilization microbiology. Consideration is given to how such methods may limit the ability to fully appreciate the inactivation kinetics of a sterilization process such as vaporized hydrogen peroxide (VH2O2) sterilization, and consequently design efficient sterilization processes. Specific use of the real-time flow cytometry (FCM) is described by way of elucidating the practical relevance of these limitation factors with implications and opportunities for the sterilization industry discussed. Application of FCM to address these culture-based limitation factors will inform real-time kinetic inactivation modelling and unlock potential to embrace emerging opportunities for pharma, medical device and sterilization industries including potentially disruptive applications that may involve reduced usage of sterilant.

Water reclamation and reuse

Literature published in 2019 pertinent to water reclamation and reuse has been classified into five sections: safe reuse, treatment technologies, management, assessment, and case studies. Membranes have been widely applied in integrated processes to polish secondary effluent and achieve high-quality reclaimed water. Increased efforts have also been made to facilitate feasible and safe water reuse. PRACTITIONER POINTS: This article summarizes literature published in 2019 pertinent to water reclamation and reuse. Water reclamation and reuse can be classfied into five sections: safe reuse, treatment technology, management, assessment, and case studies. Membranes were widely used in integrated processes for the production of high-quality reclaimed water.

Computational flow cytometry of planktonic populations for the evaluation of microbiological-control programs in district cooling plants

Biofouling poses a serious concern for the district cooling (DC) industry. Current industry practises for monitoring biofouling continue to rely on culture-based methods for microbial enumeration, which are ultimately flawed. Computational flow cytometric (cFCM) analyses, which offer enhanced reproducibility and streamlined analytics versus conventional flow cytometry were applied to samples taken from 3 sites in each of 3 plants over a 5-week sampling program. We asked whether the application of cFCM to monitoring planktonic community dynamics in DC plants could be able to provide sufficient information to enhance microbiological-control strategies at site and inform about plant performance impacts. The use of cFCM enabled the evaluation of biocide dosing, deep cleaning treatment efficiencies and routes of microbial ingress into the studied systems. Additionally, inherent risks arising from the reintroduction of microbiological communities into recently cleaned WCT basins from contaminated cooling waters were identified. However, short-term dynamics did not relate with plant performance metrics. In summary, the insights offered by this approach can inform on plant status, enable evaluations of microbial loads during biofouling mitigation programs and, ultimately, enhance industry management of the biofouling process.

Microwave-induced release and degradation of airborne antibiotic resistance genes (ARGs) from Escherichia coli bioaerosol based on microwave absorbing material

Antibiotic resistance genes (ARGs) have been detected in the atmosphere. Airborne ARGs transmission threatens human health. In the present study, we investigated the release and degradation of airborne ARGs from Escherichia coli bioaerosol through microwave (MW) irradiation. In this study, a new MW absorbing material (Fe₃O₄@SiC ceramic foam) that contributed to its stronger MW absorption is presented. When the MW input energy density was 7.4 × 10³ kJ/m³, the concentration of airborne Escherichia coli decreased by 4.4 log. Different DNA forms were found in the air because MW irradiation ruptured cell membranes. The bound particles provide more protection for bound DNA in the degradation process than free DNA. After the self-degradation of the released airborne free ARGs, some of them would remain and continue to spread in the atmosphere. The released airborne free ARGs cannot be ignored. Total ARGs concentrations decrease rapidly with increased temperature. The inactivation rate constant of ARGs through MW irradiation is higher than that through the Fenton and UV, however, the energy efficiency per order of MW irradiation is lower. Therefore, MW irradiation with Fe₃O₄@SiC ceramic foam could efficiently degrade the distribution of ARGs in the atmosphere.

Water and microbial monitoring technologies towards the near future space exploration

Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.

Reuse of ultrafiltered effluents for crop irrigation: On-site flow cytometry unveiled microbial removal patterns across a full-scale tertiary treatment

Reuse of treated wastewater for crop irrigation has been widely adopted to mitigate the effects of water scarcity on agricultural yields and to help preserving the integrity of aquatic ecosystems. This paper presents the outcomes of one-year monitoring of a full-scale agro-industrial wastewater treatment plant designed for water reuse, with a multistage tertiary treatment based on sand filtration, membrane ultrafiltration, storage and on-demand UV disinfection. We aimed to test flow cytometry as a monitoring tool to provide on-site indications on tertiary treatment performances and on the quality of treated wastewater along the treatment scheme. Membrane ultrafiltration retained prokaryotic cells and E. coli (>3 log). During storage of treated effluents, a significant decay of E. coli was observed together with the growth of prokaryotic and eukaryotic cells, and the UV disinfection was effective only against fecal indicators. The microbial quality of the treated effluent was comparable to the control groundwater locally used for irrigation. On-site rapid assessments by flow cytometry allowed unveiling crucial aspects affecting the microbiological quality of ultrafiltration permeate and treated effluent immediately after sampling, including plant operating performances and microbial removal patterns across the treatment train.

Online microbial fingerprinting for quality management of drinking water: Full-scale event detection

Microbial regrowth during drinking water distribution can result in a variety of problems such as a deviating taste and odor, and may even pose a risk to public health. Frequent monitoring is essential to anticipate events of biological instability, and relevant microbial parameters for operational control of biostability of drinking water should be developed. Here, online flow cytometry and derived biological metrics were used to assess the biological stability of a full-scale drinking water tower during normal and disturbed flow regime. Pronounced operational events, such as switching from drinking water source, and seasonal changes, were detected in the total cell counts, and regrowth was observed despite the short hydraulic residence time of 6-8 h. Based on the flow cytometric fingerprints, the Bray-Curtis dissimilarity was calculated and was developed as unambiguous parameter to indicate or warn for changing microbial drinking water quality during operational events. In the studied water tower, drastic microbial water quality changes were reflected in the Bray-Curtis dissimilarity, which demonstrates its use as an indicator to follow-up and detect microbial quality changes in practice. Hence, the Bray-Curtis dissimilarity can be used in an online setup as a straightforward parameter during full-scale operation of drinking water distribution, and combined with the cell concentration, it serves as an early-warning system for biological instability.

Flow cytometry for rapid characterisation of microbial community dynamics in waste stabilisation ponds

Algal and bacterial communities play a major role in the treatment performance and efficiency of waste stabilisation ponds (WSPs); however, the study of these WSP microbial communities has been challenging. Flow cytometry (FCM) has been used widely as a rapid, culture-independent method of characterising algae and/or bacteria in a range of freshwater and marine environments, and in conventional wastewater treatment processes, but its application to WSP wastewater has been underexplored. In this study, a method for the characterisation of both algal and bacterial microbial populations in WSP wastewater is presented and standardised, using cultures and field samples. We show that SYTO 16 dye is more effective than SYBR Green I for the concurrent detection of both algae and bacteria in samples. Through gating and phenotypic diversity analysis, the FCM results show both spatial and temporal shifts in pond microbial communities. The ability to rapidly determine the spatiotemporal shifts in pond populations is not only important for the improvement of pond operation and monitoring strategies, but also for the planning and management. Flow cytometry has the potential to become a diagnostic tool for ponds to assess treatment performance and determine the most optimal operating conditions.

Effect of micro-aerobic process on improvement of anaerobic digestion sewage sludge treatment: flow cytometry and ATP assessment

Micro-aeration as a pretreatment method improves the efficiency of anaerobic digestion of municipal sewage sludge and consequently promotes the methane production. In this study, adenosine triphosphate (ATP) and flow cytometry (FCM) were employed to monitor the performance of the micro-aerobic process and investigate the survival of bacterial cells within the process. At first, the effect of air flow rate (AFR) (0.1, 0.2, 0.3 and 0.5 vvm) on hydrolysis of mixed sludge in 5 aeration cycles (20, 30, 40, 48 and 60 hours) was examined. Then, the effects of the micro aerobic process on methane (CH₄) production in anaerobic digestion were surveyed. The highest VSS reduction was 30.6% and 10.4% for 40 hours in the reactor and control, respectively. Soluble COD also fluctuated between 40.87 and 65.14% in micro-aerobic conditions; the highest SCOD was achieved at the time of 40 h. Microbial activities were increased by 597%, 170% and 79.4% for 20, 30 and 40 h pretreatment with the micro-aerobic process, respectively. Apoptosis assay showed that micro-aerobic pre-treatment at 20, 30 and 40 h increased the percentage of living cells by 57.4, 62.8 and 67.9%, respectively. On the other hand, FCM results showed that the highest percentage of viable bacteria (i.e., 67.9%) was observed at 40 h pretreating which was approximately 40% higher the ones for the control. Variation in cumulative methane production shows that methane production was increased by 221% compared to anaerobic digestion (control group). Therefore, ATP and FCM can be employed as two appropriate, accurate, relatively specific indicators for monitoring the process and bacteria viability.

Micro-aeration as a pretreatment method improves the efficiency of anaerobic digestion of municipal sewage sludge and consequently promotes the methane production.

Single-cell impedance analysis of osteogenic differentiation by droplet-based microfluidics

Single-cell analysis is critical to understanding its heterogeneity and biological processes, such as stem cell differentiation, and elucidating the underlying mechanisms of cellular metabolism. New tools to promote intercellular variability studies help elucidate cellular regulation mechanisms. Here an impedance measurement and analysis system was built to monitor the osteogenic differentiation of single bone marrow mesenchymal stem cells (BM-MSCs) in droplets. The biochip including a microelectrode array was designed based on droplet microfluidics and fabricated. A novel theoretical electrical model was proposed to simulate the electrical properties of cells in the droplets. Impedance measurements showed that single cells are substantially heterogeneous during osteoblast differentiation at different stages (days 0, 7, 14 and 21) and different cell passages (passages 6, 7 and 11). This result was consistent with the appearance of two biomarkers (alkaline phosphatase and calcium nodules), which are the gold standard biomarkers of osteoblastogenesis and differentiation. The device enabled highly efficient single-cell trapping, accurate positioning, and sensitive, label-free and noninvasive impedance measurements of individual cells with multiple channels. This system provides a strategy for exploring the processes of osteoblastogenesis and differentiation at the single-cell level and has substantial potential for applications in the biomedical field.