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High nutrient loading into groundwater and surface water systems has deleterious impacts on the environment, such as eutrophication, decimation of fish populations, and oxygen depletion. Conventional onsite wastewater treatment systems (OWTS) and various waste streams with high ammonium (NH4+) concentrations present a challenge, due the inconsistent performance of environmental biotechnologies aimed at managing nutrients from these sources. Biological nitrogen removal (BNR) is commonly used in batch or packed-bed reactor configurations for nitrogen removal from various waste streams. In recognition of the need for resource recovery, algal photobioreactors are another type of environmental biotechnology with the potential for simultaneously treating wastewater while recovering energy. However, irrespective of the technology adopted, outstanding issues remain that affect the consistent performance of environmental biotechnologies for nitrogen removal and resource recovery. In OWTS, transient loading can lead to inconsistent nitrogen removal efficiency, while the presence of high free ammonia (FA) can exert inhibitory effects on microorganisms that mediate transformation of nitrogen species as well as microalgae that utilize nitrogen. Therefore, to overcome these challenges there have been experimental studies investigating the addition of adsorption and ion exchange (IX) media that can temporarily take up specific nitrogen ions. Bioreactors comprised of microorganisms and adsorption/IX media can attenuate transient loading as well as mitigate inhibitory effects on microorganisms and microalgae; however, the interplay between physicochemical and processes in these systems is not well understood. Therefore, the main objective of this dissertation was to develop theoretical and numerical models that elucidate the complex interactions that influence the fate of chemical species in the bioreactors. To achieve this objective and address the issues related to improving the understanding of the underlying mechanisms occurring within the environmental biotechnologies investigated, the following three research studies were done: (i) experimental and theoretical modeling studies of an IX-assisted nitrification process for treatment of high NH4+ strength wastewater (Chapter 3), (ii) theoretical and numerical modeling of a hybrid algal photosynthesis and ion exchange (HAPIX) process for NH4+ removal and resource recovery (Chapter 4), and (iii) mathematical and numerical modeling of a mixotrophic denitrification process for nitrate (NO3-) removal under transient inflow conditions (Chapter 5). The experimental results for the IX-assisted nitrification process showed that by amending the bioreactor with zeolite, there was a marked increase in the nitrification rate as evidenced by an increase in NO3– production from an initial concentration of 3.7 mg-N L-1 to 160 mg-N L-1. This increase is approximately an order of magnitude greater than the increase in the reactor without chabazite. Therefore, the experimental studies provided support for the hypothesis that IX enhances the nitrification process. To garner further support for the hypothesis and better understand the mechanisms in the bioreactor, a novel mathematical model was developed that mechanistically describes IX kinetics by surface diffusion coupled with a nitrification inhibition model described by the Andrews equation. The agreement between the model and data suggests that the mathematical model developed provides a theoretically sound conceptual understanding of IX-assisted nitrification. A model based on the physics of Fickian diffusion, IX chemistry, and algal growth with co-limiting factors including NH4+, light irradiance, and temperature was developed to describe a batch reactor comprised of microalgae and zeolite. The model can reproduce the temporal history of NH4+ in the reactor as well as the growth of microalgae biomass. The mathematical model developed for the HAPIX process balances between simplicity and accuracy to provide a sound theoretical framework for mechanisms involved. In OWTS, transient inflow conditions have an influence on the performance of environmental biotechnologies for nitrogen removal. Prior experiments have shown that for denitrification, a tire-sulfur hybrid adsorption and denitrification (T-SHAD) bioreactor consistently removes nitrogen under varying influent flow and concentration conditions. To enhance the understanding of the underlying mechanisms in the T-SHAD bioreactor, a mathematical model describing mass transport of NO3- and SO42- in the aqueous phase and mixotrophic denitrification was developed. Additionally, a numerical tool to solve the mathematical model was implemented and compared to previously conducted experiments. Results from the numerical simulations capture the trend of the experimental data showing approximately 90% NO3- -N removal under varying flow conditions. Moreover, the model describes the effluent characteristics of the process showing a transient response in correspondence the changes in fluid velocity. The new tools developed provide new insight into the underlying mechanisms of physical, chemical, and biological processes within these bioreactors. The tools developed in this dissertation have a potential broad impact in environmental biotechnology for wastewater treatment in on-site systems, for treatment of high strength wastewater, and can be extended easily for stormwater management systems aimed at mitigating high nutrient loading to the environment.

Increasing nitrate concentration in ground water from improper disposal of sewage and excessive use of fertilizers is deleterious to human health as ingestion of nitrate contaminated water can cause methaemoglobinemia in infants and possibly cancer in adults. The permissible limit for nitrate in potable water is 45 mg/L. Unacceptable levels of nitrate in groundwater is an important environmental issue as nearly 80 % of Indian rural population depends on groundwater as source of drinking water. Though numerous technologies such as reverse osmosis, ion exchange, electro-dialysis, permeable reactive barriers using zero-valent iron exists, nitrate removal from water using affordable, sustainable technology, continues to be a challenging issue as nitrate ion is not amenable to precipitation or removable by mineral adsorbents. Tapping the denitrification potential of soil denitrifiers which are inherently available in the soil matrix is a possible sustainable approach to remove nitrate from contaminated drinking water. Insitu denitrification is a useful process to remove NO3–N from water and wastewater. In biological denitrification, nitrate ions function as terminal electron acceptor instead of oxygen; the carbon source serve as electron donor and the energy generated in the redox process is utilized for microbial cell growth and maintenance. In this process, microorganisms first reduce nitrate to nitrite and then produce nitric oxide, nitrous oxide, and nitrogen gas. The pathway for nitrate reduction can be written as: NO3-→ NO2-→ NO → N2O → N2. (i) Insitu denitrification process occurring in soil environments that utilizes indigenous soil microbes is the chosen technique for nitrate removal from drinking water in this thesis. As presence of clay in soil promotes bacterial activity, bentonite clay was mixed with natural sand and this mix, referred as bentonite enhanced sand (BES) acted as the habitat for the denitrifying bacteria. Nitrate reduction experiments were carried out in batch studies using laboratory prepared nitrate contaminated water spiked with ethanol; the batch studies examined the mechanisms, kinetics and parameters influencing the heterotrophic denitrification process. Optimum conditions for effective nitrate removal by sand and bentonite enhanced sand (BES) were evaluated. Heterotrophic denitrification reactors were constructed with sand and BES as porous media and the efficiency of these reactors in removing nitrate from contaminated water was studied. Batch experiments were performed at 40°C with sand and bentonite enhanced sand specimens that were wetted with nutrient solution containing 22.6 mg of nitrate-nitrogen and ethanol to give C/N ratio of 3. The moist sand and BES specimens were incubated for periods ranging from 0 to 48 h. During nitrate reduction, nitrite ions were formed as intermediate by-product and were converted to gaseous nitrogen. There was little formation of ammonium ions in the soil–water extract during reduction of nitrate ions. Hence it was inferred that nitrate reduction occurred by denitrification than through dissimilatory nitrate reduction to ammonium (DNRA). The reduction in nitrate concentration with time was fitted into rate equations and was observed to follow first order kinetics with a rate constant of 0.118 h-1 at 40°C. Results of batch studies also showed that the first order rate constant for nitrate reduction decreased to 5.3x10-2 h-1 for sand and 4.3 x10-2 h-1 for bentonite-enhanced sand (BES) at 25°C. Changes in pH, redox potential and dissolved oxygen in the soil-solution extract served as indicators of nitrate reduction process. The nitrate reduction process was associated with increasing pH and decreasing redox potential. The oxygen depletion process followed first order kinetics with a rate constant of 0.26 h-1. From the first order rate equation of oxygen depletion process, the nitrate reduction lag time was computed to be 12.8 h for bentonite enhanced sand specimens. Ethanol added as an electron donor formed acetate ions as an intermediate by-product that converted to bicarbonate ions; one mole of nitrate reduction generated 1.93 moles of bicarbonate ions that increased the pH of the soil-solution extract. The alkaline pH of BES specimen (8.78) rendered it an ideal substrate for soil denitrification process. In addition, the ability of bentonite to stimulate respiration by maintaining adequate levels of pH for sustained bacterial growth and protected bacteria in its microsites against the effect of hypertonic osmotic pressures, promoting the rate of denitrification. Buffering capacity of bentonite was mainly due to high cation exchange capacity of the clay. The presence of small pores in BES specimens increased the water retention capacity that aided in quick onset of anaerobiosis within the soil microsites. The biochemical process of nitrate reduction was affected by physical parameters such as bentonite content, water content, and temperature and chemical parameters such as C/N ratio, initial nitrate concentration and presence of indigenous micro-organisms in contaminated water. The rate of nitrate reduction process progressively increased with bentonite content but the presence of bentonite retarded the conversion of nitrite ions to nitrogen gas, hence there was significant accumulation of nitrite ions with increase in bentonite content. The dependence of nitrate reduction process on water content was controlled by the degree of saturation of the soil specimens. The rate of nitrate reduction process increased with water content until the specimens were saturated. The threshold water content for nitrate reduction process for sand and bentonite enhanced sand specimens was observed to be 50 %. The rate of nitrate reduction linearly increased with C/N ratio till steady state was attained. The optimum C/N ratio was 3 for sand and bentonite enhanced sand specimens. The activation energy (Ea) for this biochemical reaction was 35.72 and 47.12 kJmol-1 for sand and BES specimen respectively. The temperature coefficient (Q10) is a measure of the rate of change of a biological or chemical system as a consequence of increasing the temperature by 10°C. The temperature coefficient of sand and BES specimen was 2.0 and 2.05 respectively in the 15–25°C range; the temperature coefficients of sand and BES specimens were 1.62 and 1.77 respectively in the 25–40°C range. The rate of nitrate reduction linearly decreased with increase in initial nitrate concentration. The biochemical process of nitrate reduction was unaffected by presence of co-ions and nutrients such as phosphorus but was influenced by presence of pathogenic bacteria. Since nitrate leaching from agricultural lands is the main source of nitrate contamination in ground water, batch experiments were performed to examine the role of vadose (unsaturated soil) zone in the nitrate mitigation by employing sand and BES specimens with varying degree of soil saturation and C/N ratio as controlling parameters. Batch studies with sand and BES specimens showed that the incubation period required to reduce nitrate concentrations below 45 mg/L (t45) strongly depends on degree of saturation when there is inadequate carbon source available to support denitrifying bacteria; once optimum C/N ratio is provided, the rate of denitrification becomes independent of degree of soil saturation. The theoretical lag time (lag time refers to the period that is required for denitrification to commence) for nitrate reduction for sand specimens at Sr= 81 and 90%, C/N ratio = 3 and temperature = 40ºC corresponded to 24.4 h and 23.1 h respectively. The lag time for BES specimens at Sr = 84 and 100%, C/N ratio = 3 and temperature = 40ºC corresponded to 13.9 h and 12.8 h respectively. Though the theoretically computed nitrate reduction lag time for BES specimens was nearly half of sand specimens, it was experimentally observed that nitrate reduction proceeds immediately without any lag phase in sand and BES specimens suggesting the simultaneous occurrence of anaerobic microsites in both. Denitrification soil columns (height = 5 cm and diameter = 8.2 cm) were constructed using sand and bentonite-enhanced sand as porous reactor media. The columns were permeated with nitrate spiked solutions (100 mg/L) and the outflow was monitored for various chemical parameters. The sand denitrification column (packing density of 1.3 Mg/m3) showed low nitrate removal efficiency because of low hydraulic residence time (1.32 h) and absence of carbon source. A modified sand denitrification column constructed with higher packing density (1.52 Mg/m3) and ethanol addition to the influent nitrate solution improved the reactor performance such that near complete nitrate removal was achieved after passage of 50 pore volumes. In comparison, the BES denitrification column achieved 87.3% nitrate removal after the passage of 28.9 pore volumes, corresponding to 86 h of operation of the BES reactor. This period represents the maturation period of bentonite enhanced sand bed containing 10 % bentonite content. Though nitrate reduction is favored by sand bed containing 10 % bentonite, the low flow rate (20-25 cm3/h) impedes its use for large scale removal of nitrate from drinking water. Hence new reactor was designed using lower bentonite content of 5 % that required maturation period of 9.6 h. The 5 and 10 % bentonite-enhanced sand reactors bed required shorter maturation period than sand reactor as presence of bentonite contributes to increase in hydraulic retention time of nitrate within the reactor. On continued operation of the BES reactors, reduction in flow rate from blocking of pores by microbial growth on soil particles and accumulation of gas molecules was observed that was resolved by backwashing the reactors.