Attached growth biological processes offer advantages over traditional water purification technologies through high biomass retention, easy sludge-water separation, multiple multispecies synergies in proximity, resilience to shock loading, low space requirements, and reactor operational flexibility. Traditionally, attached growth refers to biofilms that require abiotic carrying media for bacteria to attach and grow on. While biofilms have been broadly applied in wastewater treatment, its potential for potable reuse or stormwater treatment has not been well studied. The treatment trains of pre-ozonation followed by biologically active filtration (ozone- BAF) is an advanced biofilm technology for potable reuse that can generate high-quality potable water at reduced energy and chemical demands by removing pollutant through three different pathways: oxidation, adsorption, and biodegradation. However, these pathways can result in both desirable and undesirable effects, and the mechanism behind it is still unclear. To understand the mechanisms of various pollutant removal, parallel performance comparisons of ozone-BAF treatment trains with spent and regenerated granular activated carbon (GAC), along with a range of pre-oxidant ozone doses were performed. Another common issue of BAF is the headloss buildup during its operation, which has become a significant energy and maintenance burden at many utilities. Thus, a mathematical model was developed to predict BAF headloss buildup in response to organic removal and nitrification. For stormwater treatment, the feasibility of using biofilms for stormwater biological nitrogen removal (BNR) is still largely unknown, as very limited research effort has been dedicated to this aspect. Thus, a mathematical model was developed to evaluate the potential of using BNR techniques for stormwater nitrogen removal. Aerobic granules are an even more advanced attached growth process, which eliminates the need for abiotic carrying media. So far, aerobic granular sludge is only formed in sequential batch reactors but not in a continuous flow system. Therefore, continuous flow aerobic granulation from traditional activated sludge was investigated and, for the first time, successfully achieved in continuous flow plug-flow bioreactors fed with real municipal wastewater. Besides, the role and critical value of an essential operational parameter, feast/famine ratio, for continuous flow aerobic granulation were determined. / Doctor of Philosophy / Water scarcity and increasing water demand caused by urban population growth and climate change is a reality throughout the world. Thus, process intensification of the current water and wastewater technologies is gaining increasing attention globally. Comparing to traditional water purification technologies, attached growth biological processes offers advantages such as high biomass retention, easy sludge-water separation, multiple multispecies synergies in proximity, resilience to shock loading, small footprint requirement, and reactor operational flexibility. Traditionally, attached growth refers to biofilms that require abiotic carrying media for bacteria to attach and grow on. While biofilms have been broadly applied in wastewater treatment, its potential for potable reuse or stormwater treatment has not been well studied. For potable reuse, the treatment trains of pre-ozonation followed by biologically active filtration (ozone-BAF) is an advanced biofilm technology that can generate high-quality potable water at reduced energy and chemical demands by removing pollutant through different pathways. However, the mechanism behind it is still unclear. To understand the mechanisms of various pollutant removal, parallel performance comparisons of ozone-BAF treatment trains operated with different operational conditions were performed in this dissertation. Another common issue of BAF is the headloss buildup during its operation, which has become a significant energy and maintenance burden at many utilities. Thus, a mathematical model was developed to predict the headloss buildup during BAF operation. For stormwater treatment, the feasibility of using biofilms for stormwater biological nitrogen removal (BNR) is still largely unknown, as very limited research effort has been dedicated to this aspect. Thus, a mathematical model was developed to evaluate the potential of using BNR technique for stormwater. Aerobic granules are an even more advanced attached growth process. However, aerobic granular sludge is so far only formed in sequential batch reactors which are incompatible with the continuous flow nature of most wastewater treatment plants. Therefore, aerobic granulation from traditional activated sludge was investigated and, for the first time, successfully achieved in continuous flow plug-flow bioreactors fed with real municipal wastewater. Besides, the role of an essential operational parameter, feast/famine ratio, for continuous flow aerobic granulation was determined.

Soil aquifer treatment (SAT) during managed aquifer recharge has been studied as a method of providing additional environmental barriers to pathogens and contaminants in indirect potable reuse (IPR) applications. A soil column study was conducted by Hampton Roads Sanitation District in order to evaluate the effectiveness of SAT, as a component of its IPR project involving the replenishment of the Potomac Aquifer System (PAS), in providing a sustainable source of drinking water. Four packed soil columns were constructed with sand from the PAS and were designed to simulate the travel time of 3 days and 30 days. The tests conducted aimed at evaluating pathogen removal (MS2, E. coli and Cryptosporidium oocysts); evaluating attenuation of regulated (nitrate, nitrite, bromate, trihalomethane (THM), haloacetic acids (HAA), organic carbon) and unregulated contaminants of concern that affect drinking water quality. Effective pathogen removal was observed with 6 to 7-log removals of MS2 and E. coli and 3 to 5-log removals of microbeads, used as a surrogate for Cryptosporidium. Removal across 3 day columns was comparable to 30-day columns but the potential to achieve higher removal with longer retention time was acknowledged. Nitrate, bromate, THMs and HAAs were completely reduced in 30-day columns. Total organic carbon was removed at 25 – 35% in all four columns. Seven out of the 106 contaminants of emerging concern (CEC) tested were consistently detected in the column feed and effluent at concentrations greater than 100 ng/L; some compounds showed potential for removal while no conclusive results were drawn for the remaining compounds. / MS / Potable reuse is a sustainable solution to the increasing water demands of the present and more so the future. Hampton Road Sanitation District (HRSD) aims to treat effluent from its wastewater treatment plants using advanced treatment process for direct recharge of the Potomac aquifer system. This is a method of indirect potable reuse termed as managed aquifer recharge (MAR). MAR can provide additional environmental barriers to contaminants present in water through a process of natural attenuation called soil aquifer treatment (SAT). A soil column study was conducted at HRSD’s pilot scale facility in order to asses SAT under controlled conditions at a meaningful scale. Attenuation of pathogens; regulated contaminants (nitrate, nitrite, bromate, etc.) and contaminants of emerging concern was evaluated through the soil columns. The results showed effective removal of most contaminants of interest which demonstrated that SAT potentially improves water quality and meets public health standards in potable reuse applications.

The Potomac River Basin is significant for both public and ecological health as it flows directly into the ecologically-sensitive Chesapeake Bay. It is a drinking water source for about 5 million people living in Maryland, Virginia, and Washington D.C. The discovery of intersex fish, an indicator of poor ecological health, in the Chesapeake Bay occurred in the 2000s, and has led to a series of studies in the watershed to determine the sources and magnitude of endocrine disruption. Endocrine disrupting compounds (EDCs) are exogenous chemicals that interfere with the endocrine system and can cause detrimental health effects at low concentrations. This study aims to understand a best management practice referred to as planned indirect potable reuse (IPR) and its impacts on EDCs. The Occoquan Watershed is a planned IPR subwatershed of the Potomac River Basin. Water samples were collected at the water reclamation plant discharge (Upper Occoquan Service Authority), up- and downstream of that location along Bull Run, and at the water treatment plant intake (Frederick P. Griffith WTP) in the Occoquan Watershed to assess planned IPR. Samples were also collected at a water treatment plant (James J. Corbalis WTP) along the Potomac River for comparison as an unplanned IPR location. These two groups of samples were analyzed for EDCs (categorized into two groups: estrogen hormones and other synthetic organic compounds (SOCs)), nutrients, and other water quality parameters. The infrequency of estrogen hormones and SOC patterns indicate planned and unplanned IPR are both viable approaches to provide safe drinking water / Master of Science / Our river systems are important to maintain both for human and environmental health. The Potomac River Basin is the area of land drained by the Potomac River and its tributaries. The Potomac River Basin is significant for both public and ecological health as it flows directly into the ecologically-sensitive Chesapeake Bay. It is a drinking water source for about 5 million people living in Maryland, Virginia, and Washington D.C. The discovery of intersex fish, or when a single fish has both male and female characteristics, occurred in the Chesapeake Bay in the 2000s. Fish health is often an indicator of poor environmental health, and in this case endocrine disruption. This discovery led to a series of studies in the watershed to determine the sources and magnitude of endocrine disruption. Endocrine disrupting compounds (EDCs) are external chemicals that interfere with the endocrine system once they enter the body of a human or another organism, and can cause detrimental health effects even at low concentrations. This study aims to understand a best management practice, or a type of water pollution control, referred to as planned indirect potable reuse (IPR) and its impacts on EDCs. IPR occurs when wastewater from a community is discharged into to a river or a reservoir, and then downstream it is withdrawn from that same source for drinking water purposes. This can be either planned or unplanned. Planned IPR is becoming more common as population, especially in urban areas, increases. The Occoquan Watershed is a planned IPR subwatershed of the Potomac River Basin. Water samples were collected at the water reclamation plant discharge (Upper Occoquan Service Authority), up- and downstream of that location along Bull Run, and at the water treatment plant intake (Frederick P. Griffith WTP) in the Occoquan Watershed to assess planned IPR. Samples were also collected at a water treatment plant (James J. Corbalis WTP) along the Potomac River for comparison as an unplanned IPR location. These two groups of samples were analyzed for EDCs (categorized into two groups: estrogen hormones and other synthetic organic compounds (SOCs)), nutrients, and other water quality parameters. The infrequency of estrogen hormones and SOC patterns indicate planned and unplanned IPR are both viable approaches to provide safe drinking water.

In an era of pervasive water stress caused by population growth, urbanization, drought, and climate change, limiting the dissemination of microbial contaminants of emerging concern (MCECs) is of the utmost importance for the protection of public health. In this dissertation, two important subsets of MCECs, opportunistic pathogens (OP) and antibiotic resistant genes (ARG), are studied across several compartments of the urban water cycle, including surface water, stormwater, wastewater, recycled water, and potable water. Collectively, this dissertation advances knowledge about the occurrence of OPs and ARGs across these water systems and highlights trends that may be of value in developing management strategies for limiting their regrowth and transmission. Field studies of two surface water catchments impacted by stormwater runoff demonstrated the prevalence of ARGs in urban stormwater compared to pristine, unimpacted sites, or to days when no precipitation was recorded. The role of wastewater reuse in transmitting OPs and ARGs was also investigated. Traditional tertiary wastewater treatment plants producing water for non-potable use were found to be largely ineffective at removing ARGs, but plants using advanced oxidation processes or ozonation paired with biofiltration to produce direct potable reuse water were highly effective at removing ARGs. Non-potable reclaimed water consistently had greater quantities of sul1, a sulfonamide ARG, and Legionella and Mycobacterium, two OPs of significant public health concern, present than corresponding potable systems. Limited regrowth of OPs and ARGs did occur in simulated premise (i.e., building) plumbing systems operated with direct potable reuse waters, but regrowth was comparable to that observed in systems fed with potable water derived from surface or groundwater. Advancements were also made in understanding the role of several hypothesized driving forces shaping the antibiotic resistome in natural and engineered water systems: selection by antimicrobials and other compounds, horizontal gene transfer, and microbial community composition. Finally, whole-genome and metagenomic characterization were applied together towards profiling L. pneumophila in clinical and water samples collected from Flint, Michigan, where an economically-motivated switch to an alternative water source created conditions favorable for growth of this organism and likely triggered one of the largest Legionnaires' Disease outbreaks in U.S. history. / PHD / Population growth, urbanization, drought, and climate change have all driven many U.S. municipalities to utilize alternative water sources, such as recycled wastewater, to offset demand on traditional potable water sources. Many water providers have moved towards a modern paradigm of utilizing multiple available water sources, recognizing the interconnectedness of various components of the urban water cycle, leading to opportunities to improve sustainability, optimize infrastructure use, stimulate economic growth, increase coordination among water agencies, and identify new water resources from which to meet consumer needs. Though advancements in treatment technologies throughout the twentieth century have largely succeeded in eliminating waterborne disease outbreaks associated with contamination of municipal water supplies by fecal pathogens in developed countries, several microbial contaminants of emerging concern (MCECs) have garnered attention. Two major groups of MCECs are considered in this dissertation: antibiotic resistance, including antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG), and opportunistic pathogens (OP), such as Legionella pneumophila, the causative agent of Legionnaires’ Disease. ARB are a rising cause of disease around the world and are a major challenge to modern medicine because they make antibiotics used for treatment ineffective. OPs, the leading cause of waterborne disease in the U.S. and other developed countries, have become prevalent in engineered water systems where low nutrient concentrations, warm water temperatures, and long stagnation times can facilitate their growth. Immunocompromised people, including smokers and the elderly, are especially vulnerable to infection with OPs. The role of the urban water cycle in facilitating the spread of these MCECs is not well understood. Here they were studied across several compartments of the urban water cycle, including surface water, stormwater, wastewater, recycled water (spanning a variety of intended uses, from non-potable to direct potable reuse), and potable water. Field studies were conducted of two watersheds impacted by stormwater runoff, one in the arid Colorado Front Range under conditions of a rare, 1-in-1,000 year rainfall event, and one in the humid climate of southwest Virginia, during three summer storms. Both studies demonstrated the prevalence of ARGs in urban stormwater compared to pristine, unimpacted sites, or to days when no precipitation was recorded. The role of wastewater reuse in transmitting OPs and ARGs was also investigated. Wastewater treatment plants producing water for non-potable use (i.e. applications such as irrigation, but not for human consumption) were found to be largely inefficient at removing ARGs, and this reclaimed water consistently had greater quantities of the sul1 ARG present than in corresponding potable systems. In these systems, genes associated with the OPs Legionella and Mycobacterium as well as total bacteria were more abundant in reclaimed water than in corresponding potable systems. In more advanced treatment plants utilizing advanced oxidation processes or ozonation paired with biofiltration to produce direct potable reuse water (i.e. water fit for human consumption), ARGs were very effectively removed by treatment, with abundances often found to be higher in corresponding potable waters derived from surface or groundwater. Limited regrowth of ARGs as well as OPs did occur in simulated home plumbing systems operated with these waters, but regrowth was comparable to that observed in systems fed with potable water derived from surface or groundwater. Finally, a study of L. pneumophila in the Flint, Michigan drinking water system during use of an alternative water source that has been identified as a likely cause of two Legionnaires’ Disease outbreaks revealed presence of multiple strains of the OP in the system. Genomic comparisons revealed that strains isolated from hospital and residential water samples were highly similar to clinical strains associated with the outbreaks. Advancements were also made in understanding the role of several hypothesized driving forces in shaping the antibiotic resistome in natural and engineered water systems: selection by antimicrobials and other compounds, horizontal gene transfer, and microbial community composition. Together, these chapters describe an advancement in knowledge regarding the occurrence of OPs and ARGs in a variety of water systems, and highlight trends that may be of value in developing management strategies for limiting regrowth or transmission of these bacteria in various compartments of the urban water cycle.

No description available.

Indirect potable reuse has been practiced with the potential to enhance sustainability of water resources if planned accordingly. Depending on the pretreatment implemented for potable reuse, emerging contaminants; such as pharmaceuticals, personal care products, industrial solvents, bacterial/viral pathogens, and disinfection byproducts, might be present in source water and difficult to remove via various water treatment technologies. Low molecular weight organic compounds are especially challenging to remove and may require treatment optimization. The overarching purpose of this study was to demonstrate the feasibility of a carbon-based advanced treatment train; including ozonation, biological activated carbon (BAC) filtration and granular activated carbon (GAC) adsorption to achieve water quality suitable for potable reuse and assess the impact of a range of operating conditions for emerging contaminant removal at pilot-scale. The results from this study showed that carbon-based treatment train is equally effective as more commonly used, and more costly, membrane-based treatment trains in terms of pathogen and disinfection byproduct removal. A multiple-barrier approach was implemented, with each treatment stage capable of removing total organic carbon (TOC). GAC was responsible for removal of most of the TOC and emerging contaminants and this removal depended on the number of bed volumes of water processed by GAC. Empty bed contact time was another factor that dictated the extent of TOC removal in the BAC and GAC units as the carbon media was exhausted. Among the emerging contaminants detected, sucralose, iohexol and acesulfame-k were present in the highest concentrations in the influent and were detected consistently in the GAC effluent, thus making them good indicators of treatment performance. Apart from organics removal, BAC played an important role in removal of nutrients, such as ammonia via nitrification. N-Nitrosodimethlyamine (NDMA) was formed in the treatment process by ozone, but was shown to be effectively removed by BAC. EBCT, temperature, ozone dose and presence of pre-oxidants, such as monochloramine, played an important role in determining the amount of NDMA removed. These factors can be further optimized to improve NDMA removal. Sodium bisulfite was used for dechlorinating monochloramine residual post ozone. Nitrification in the BAC was shown to be inhibited by excess of sodium bisulfite dose. Thus monochloramine residual needs to be dechlorinated with sodium bisulfite to help with NDMA degradation but at the same time the sodium bisulfite dose needs to be monitored to allow complete nitrification in the BAC. 1,4-dioxane, another contaminant of emerging concern, was monitored in the treatment process. Biodegradation of 1,4-dioxane was enhanced via addition of tetrahydrofuran as a growth substrate. Biodegradation of 1,4-dioxane can help reduce energy and capital costs associated with advanced oxidation processes that are currently used for 1,4-dioxane removal. Further, relying on biodegradation for the removal of 1,4-dioxane can help avoid the formation of disinfection byproducts associated with advanced oxidation processes such as ozone with peroxide or ultraviolet disinfection with peroxide. The results from this project can be useful for designing potable reuse treatment trains and provide a baseline for removal of organic carbon and emerging contaminants. The conventionally used reverse osmosis and ultrafiltration approach is useful for organics removal in areas where the rationale behind potable reuse is water scarcity. Operational difficulties encountered during this study can prove to be important as this treatment process is scaled up to treat a total of 120 MGD of water for managed aquifer recharge. Overall the lessons learnt from this study can give a better understanding of a carbon-based treatment and further the advancement of reuse projects that have drivers other than water scarcity. / Doctor of Philosophy / The increased growth in urban areas has been accompanied by an increase in potable water demand, leading to depletion of surface and groundwater. Further, the discharge of nutrients such as nitrogen and phosphorus into some of these water bodies can lead to algal blooms. Water reuse involves treating used water and discharging into either a surface or groundwater body. Water reuse has been sought after as a solution to prevent these nutrients being discharged into surface water and to provide a sustainable solution for depletion of water sources. Direct or indirect potable reuse can include a combination of advanced treatment methods such as membrane filtration using ultrafiltration and reverse osmosis, biological filtration, granular or powdered activated carbon adsorption and disinfection methods such as ozonation and ultraviolet disinfection. This study focused on Hampton Roads Sanitation District's managed aquifer recharge project 'sustainable water initiative for tomorrow' (SWIFT), two different advanced water treatment strategies, namely carbon-based and membrane-based were implemented on a pilot-scale (20,000 L/day). The driver for indirect potable reuse in this study was not related to water shortage but aimed at reducing the nutrients discharged into the Chesapeake Bay. Other reasons for implementing reuse included recharging the depleting groundwater levels, land subsidence, and preventing flooding and seawater intrusion near the coastal areas. Membrane-based treatments, such as reverse osmosis, have been well established and studied for potable reuse. The less frequently used carbon-based treatment, that includes used of activated carbon for adsorption and biodegradation of organics (not involving any membrane barrier), was shown to be cost-effective and provided equal protection as that of the membrane-based system in terms of removal of pathogens. Further, since there is no membrane involved in the carbon-based treatment the energy requirements are less than that of the membrane-based treatment and concentrated brine solution is not produced, which makes it favorable for potable reuse where water scarcity is not an issue. This carbon-based treatment which included ozonation and activated carbon filtration and adsorption was further monitored and optimized for removal of organic contaminants and disinfection byproducts. Emerging contaminants such as pharmaceuticals, industrial solvents and personal care products can be harmful to human health and water ecology even at low concentrations. These contaminants are often present in wastewater effluent and can enter drinking water sources if untreated. These emerging contaminants were shown to be effectively removed by ozonation and granular activated carbon adsorption. The formation of disinfection byproducts such as N-nitrosodimethylamine in the treatment process and its removal in the biological activated carbon filtration was also monitored. The impact of temperature, presence of pre-oxidants and design factors such as ozone dose and empty bed contact time affected the removal of all these contaminants. This study provided an understanding of implementing carbon-based treatment for managed aquifer recharge for optimizing removal of bulk organic carbon and emerging contaminants. The results from this study can be utilized for designing advanced water treatment systems and can prove to be a guideline for monitoring and removing emerging contaminants.

Water reuse has become a promising alternative to alleviate stress on conventional freshwater resources in the face of population growth, sea level rise, source water depletion, eutrophication of water bodies, and climate change. Potable water reuse intentionally looks to purify wastewater effluent to drinking water quality or better through the development and implementation of advanced treatment trains. While membrane-based treatment has become a widely-adopted treatment step to meet this purpose, there is growing interest in implementing treatment trains that harness microorganisms as a more sustainable and less energy-intensive means of removing contaminants of emerging concern (CECs), through biological degradation or transformation. In this dissertation, various aspects of the operation of a microbially-active carbon-based advanced treatment train producing water intended for potable reuse are examined, including fate of dissolved organic carbon, underlying microbial populations, and functional genes are explored. Further, dynamics associated with antibiotic resistance genes (ARGs), identified as a microbially-relevant CECs, are also assessed. Overall, this dissertation advances understanding associated with the interplay between and within treatment processes as they relate to removal of various organic carbon fractions, microbially community dynamics, functional genes, and ARGs. Further, when relevant, these insights are contextualized to operational conditions, process upsets, water quality parameters, and other intended water uses within the water industry with the goal of broadening the application of advanced molecular tools beyond the scope of academic research. Specifically, this dissertation illuminates relationships among organic carbon fractions and molecular markers within an advanced treatment train employing flocculation, coagulation, and sedimentation (FlocSed), ozonation, biologically active carbon (BAC) filtration, granular active carbon (GAC) contacting, and UV disinfection. Biodegradable dissolved organic carbon (BDOC) analysis was adapted specifically as an assay relevant to assessing dissolved organic carbon biodegradability by BAC/GAC-biofilms and applied to profile biodegradable/non-biodegradable organic carbon as wastewater effluent passed through each of these treatment stages. Of particular interest was the role of ozonation in producing bioavailable organic carbon that can be effectively removed by BAC filtration. In addition to understanding the removal of fractionalized organic carbon, next generation DNA sequencing technologies (NGS) were utilized to better understand the microbial dynamics characteristic of complex microbial communities during disinfection and biological treatment. Specifically, this analysis was focused on succession and colonization of taxa, genes related to a wide range of functional interests (e.g. metabolic processes, horizontal gene transfer, DNA repair, and nitrogen cycling), and microbial CECs. Finally, NGS technologies were employed to assess the differences between a wide range of water use categories, including conventional drinking water, potable reuse, and non-potable reuse effluent's microbiomes to identify core and discriminatory taxa associated with intended water usage. The outcomes of this dissertation provide valuable information for optimizing carbon-based treatment trains as an alternative to membrane-based treatment for sustainable water reuse and also advance the application of NGS as a diagnostic tool for assessing the efficacy of various water treatment technologies for achieving treatment goals. / Doctor of Philosophy / Several factors have led to increased stress on conventional drinking water sources and widespread global water scarcity. Projections indicate that continued population growth, increased water demand, and degradation of current freshwater resources will negatively contribute to water needs and underscore the need to secure new potable (i.e. fit for human consumption) sources. Water reuse is a promising alternative to offset the growing demands on traditional potable sources and ameliorate negative consequences associated with water scarcity. Discharge of treated wastewater to marine environments is especially a lost opportunity, as the water will no longer be of value to freshwater habitats or as a drinking water source. Water reuse challenges the conventional wastewater treatment paradigm by providing advanced treatment of wastewater effluent to produce a valuable resource that can be safely used directly for either non-potable (e.g., irrigation, firefighting) or potable (i.e., drinking water) applications. The means of achieving advanced treatment of wastewater effluents can take many forms, commonly relying on the utilization of membrane filtration. However, membrane filtration is an intensive process and suffers from high initial costs, high operational costs, membrane fouling with time, and the production of a salty and difficult to dispose of waste stream. These drawbacks have motivated the water reuse industry to explore more sustainable approaches to achieving high quality effluents. One such alternative relies on the utilization of microorganisms to provide biological degradation and transformation of contaminants through a process known as biologically active filtration (BAF). Comparatively to membrane systems, BAF is more cost effective and produces significantly fewer byproducts while still producing high quality treated water for reuse. However, the range in quality of the resulting treated water has not yet been fully established, in part due to the lack of understanding of the complex microbial communities responsible for biological treatment. As water and wastewater treatment technologies have evolved over the past century, many biological treatments have remained largely 'black box' due to the lack of effective tools to identify the tens of thousands of species of microbes that inhabit a typical system and to track their dynamics with time. Instead, analysis has largely focused on basic water quality indicators. This dissertation takes important steps in advancing the implementation of the study of DNA and biodegradable organic carbon (BDOC) analysis to improve understanding of the mechanisms that drive different water reuse treatment technologies and to identify potential vulnerabilities. Insights gained through application of these tools are contextualized to observed operational conditions, process upsets, and water quality measurements. This helped to advance the use of DNA-based tools to better inform water treatment engineering practice. Specifically, this dissertation dives into the relationships between organic carbon and DNA-based markers within an advanced treatment train employing flocculation, coagulation, and sedimentation (FlocSed), ozonation, biologically active carbon (BAC) filtration, granular active carbon (GAC) contacting, and UV disinfection. Development and application of the BDOC test revealed that the bulk of organic carbon entering the treatment train is dissolved. Further, BDOC analysis served to characterize the impact of specific treatment processes and changes in operational conditions on both biodegradable and non-biodegradable organic carbon fractions. Such information can help to inform continued process optimization. Utilization of DNA-based technologies shed light on the functional capacity of microbial communities present within each stage of treatment and the fate of antibiotic resistance genes (ARGs). ARGs are of concern because, when present in human pathogens, they can result in the failure of antibiotics to cure deadly infections. Other functional genes of interest were also examined using the DNA-based analysis, including genes driving metabolic processes and nitrogen cycling that are critical to water purification during BAF treatment. Also, the DNA-based analyses made it possible to better understand the effects of disinfectants on microbes. Interestingly, some ARG types increased in relative abundance (a measure analogous to percent composition) response to treatments, such as disinfection, and others decreased. Characterization of the microbial communities and their dynamic response to changing operation conditions were also observed. For example, it was possible to characterize how the profiles of microbes changed with time, an ecological process called succession, during BAC filtration and GAC contacting. Generally, this analysis, coupled with the functional analysis, shed light on the important, divergent roles of bacterial communities on organic degradation during both BAC and GAC treatment. Finally, a study was conducted that compared the microbiome (i.e. entire microbial community) between a wide range of conventional drinking water, potable reuse water, and non-potable reuse waters. Here it was found that significant differences existed between the microbial communities of water intended for potable or non-potable usage. This work also looked to expand the application of NGS technologies beyond strictly academic research by developing the application of more advanced DNA-based tools for treatment train assessment and monitoring.