The Bryan/College Station (B/CS) region has been reported to have elevated concentrations of dissolved organic carbon (DOC) in surface water. Increased DOC concentrations are worrisome as DOC has been shown to be an energy source for the recovery and regrowth of E. coli and many watersheds are impaired by high bacteria levels. To examine the sources and fates of DOC in rural and urban regions to better understand DOC movement though the environment, seven watersheds were studied. To investigate source, streams were analyzed using diffuse reflectance near infrared spectroscopy (DR-NIR) and carbon isotopes. Fate of DOC was determined through monthly streams samples, gathered between March 2011 and February 2012, which were incubated for biodegradable DOC (BDOC). Soil in the region was sampled based on land use categories. Soil was analyzed for DOC and BDOC as well as DOC adsorption, the other major fate of DOC. Above ground vegetation was sampled in conjunction with soil and analyzed for BDOC. Data indicated that fecal matter from cliff swallows provided considerable organic material to streams in the B/CS region as shown through DR-NIR. Carbon isotope values in streams ranged from -23.5 +/- 0.7% to -26.8 +/- 0.5%. Stream spectra may be able to predict carbon isotope values in streams (Adj. R2 = 0.88). Mean annual stream DOC concentrations ranged from 11 +/- 3 mg/L to 31 +/- 12 mg/L, which represents a significant decrease in DOC between 2007 and 2011. Concurrent increases in pH and conductivity were also recorded. The decrease in DOC and the increases in pH and conductivity may be due to impacts of high sodium irrigation tap water. Biodegradable DOC was low in streams, which is likely due to DOC being present in streams in refractory forms that are resistant to microbial breakdown. Soil chemistry, including soil adsorption, was greatly influenced by sodium. The elevated adsorption coefficients and release values seen in highly developed and urban open areas can be attributed to frequent exposure to high sodium irrigation water. The results indicate that sodium is a major driver of DOC in the system. Sound management decisions concerning irrigation water chemistry and urban development might eventually emerge to protect water quality as a result of this research.

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.

Biological filtration (Biofiltration) processes have been used first in Europe and then in North America for decades, however currently there is not a good overall parameter to guide biofiltration design and operation except adopting parameters from traditional particle- removal filtration process. On the basis of the biofilm model developed by Rittmann and McCarty (1980a) and the pseudo-analytical solution for the model, Zhang and Huck (1996a) obtained an analytical solution for PF (plug flow) reactors (which can be used for biofilters approximately) after demonstrating that axial dispersion could be reasonably ignored and developed a new parameter, X*, which incorporates considerations of physical contact time, filter media particle size, kinetics, etc. A small-scale application on peers’ engineering/research data by Huck (1999) demonstrated it was a better indicator than other parameters for biofiltration performance. By collecting, screening and investigating literature on AOC, BDOC and odorous compounds removal by biofiltration process, this thesis applied the X* concept to the collected investigations to assess process performances among different target parameters, different filters and different investigations. To the author’s knowledge, this is the first such attempted comprehensive comparison of literature studies, interpreted in terms of a common parameter (X*). The wide ranges of particle sizes, EBCTs, temperatures and high diversity of pre-treatment and operation conditions for the collected cases were considered to be able to well represent biofiltration practices for studied removal targets. No significant relationship between EBCTs and removal percentages were found, indicating that EBCT alone is not able to guide biofiltration design and operation. Based on kinetics parameter comparison, BDOC removal-X* relationship was established. A new parameter, θα, was developed in this thesis to refer to estimated X* values only considering EBCT and particle size. θα parameter values were estimated by comparison of ratios of θα products ((θα)’) based on the properly chosen calculation bases. Distribution of the θα values for temperature-favored (i.e. temperature ≥15°C) AOC and BDOC removal biofiltration processes matched the established removal-X* relationship reasonably. Given the exploratory nature of this research and the complexity of attempting quantitations, fits were assessed based on visual comparison. With the assistance of supporting information and by adopting available temperature activity coefficients, temperature-adjustment coefficients for θα values were determined for the different temperature ranges. Temperature-adjusted AOC and BDOC removal-θα relationships were developed and temperature-adjusted θα parameter values for AOC and BDOC removal were also estimated. Comparisons were conducted, showing fair matches based on visual examinations, for most of the temperature ranges. No relationships were found between ozone dosages and AOC/BDOC removal percentages and the statistical analysis indicated there was significant difference of removal efficiencies between ozonated and non-ozonated influents for biofilters, suggesting ozonation may not only increase the amount of BOM for following biofilter and increase the biodegradability of bulk water; it may also increase the biodegradability of AOC and BDOC themselves. It may not be realistic to obtain the estimated θα values for MIB and geosmin removal by biofiltration. However, plotting θα product vs. removal percentage for the collected MIB and geosmin removal cases shows more positive co-relationships than EBCT-removal percentage relationships visually. A utilization factor η was proposed to guide biofilter design and operation and to assess “over-design” and “under-operated”. Biofilter over-design or under-operated is common for the collected cases. In general, examining X* (or θα, a parameter incorporating the physical components of X*) provided useful information in terms of evaluation and prediction of biodegradable organic compounds removal by biofiltration, which confirms that X* is a better parameter for biofiltration design and operation than other parameters, such as EBCT.

Biological filtration (Biofiltration) processes have been used first in Europe and then in North America for decades, however currently there is not a good overall parameter to guide biofiltration design and operation except adopting parameters from traditional particle- removal filtration process. On the basis of the biofilm model developed by Rittmann and McCarty (1980a) and the pseudo-analytical solution for the model, Zhang and Huck (1996a) obtained an analytical solution for PF (plug flow) reactors (which can be used for biofilters approximately) after demonstrating that axial dispersion could be reasonably ignored and developed a new parameter, X*, which incorporates considerations of physical contact time, filter media particle size, kinetics, etc. A small-scale application on peers’ engineering/research data by Huck (1999) demonstrated it was a better indicator than other parameters for biofiltration performance. By collecting, screening and investigating literature on AOC, BDOC and odorous compounds removal by biofiltration process, this thesis applied the X* concept to the collected investigations to assess process performances among different target parameters, different filters and different investigations. To the author’s knowledge, this is the first such attempted comprehensive comparison of literature studies, interpreted in terms of a common parameter (X*). The wide ranges of particle sizes, EBCTs, temperatures and high diversity of pre-treatment and operation conditions for the collected cases were considered to be able to well represent biofiltration practices for studied removal targets. No significant relationship between EBCTs and removal percentages were found, indicating that EBCT alone is not able to guide biofiltration design and operation. Based on kinetics parameter comparison, BDOC removal-X* relationship was established. A new parameter, θα, was developed in this thesis to refer to estimated X* values only considering EBCT and particle size. θα parameter values were estimated by comparison of ratios of θα products ((θα)’) based on the properly chosen calculation bases. Distribution of the θα values for temperature-favored (i.e. temperature ≥15°C) AOC and BDOC removal biofiltration processes matched the established removal-X* relationship reasonably. Given the exploratory nature of this research and the complexity of attempting quantitations, fits were assessed based on visual comparison. With the assistance of supporting information and by adopting available temperature activity coefficients, temperature-adjustment coefficients for θα values were determined for the different temperature ranges. Temperature-adjusted AOC and BDOC removal-θα relationships were developed and temperature-adjusted θα parameter values for AOC and BDOC removal were also estimated. Comparisons were conducted, showing fair matches based on visual examinations, for most of the temperature ranges. No relationships were found between ozone dosages and AOC/BDOC removal percentages and the statistical analysis indicated there was significant difference of removal efficiencies between ozonated and non-ozonated influents for biofilters, suggesting ozonation may not only increase the amount of BOM for following biofilter and increase the biodegradability of bulk water; it may also increase the biodegradability of AOC and BDOC themselves. It may not be realistic to obtain the estimated θα values for MIB and geosmin removal by biofiltration. However, plotting θα product vs. removal percentage for the collected MIB and geosmin removal cases shows more positive co-relationships than EBCT-removal percentage relationships visually. A utilization factor η was proposed to guide biofilter design and operation and to assess “over-design” and “under-operated”. Biofilter over-design or under-operated is common for the collected cases. In general, examining X* (or θα, a parameter incorporating the physical components of X*) provided useful information in terms of evaluation and prediction of biodegradable organic compounds removal by biofiltration, which confirms that X* is a better parameter for biofiltration design and operation than other parameters, such as EBCT.